A Phylogenetic Tree Assembled from rRNA Sequences of Almost 200 Taxa from Across the Metazoan Animals  

We use nearly-complete large-subunit and small-subunit rRNA gene sequences to assemble a phylogenetic tree of animals. This work studies the relations among the many animal phyla that originated during or before the early Cambrian, many of which are represented as fossils in the Burgess Shale. 

We calculated our tree using statistical likelihood methods after improving the gene-alignment technique to better reflect the secondary structure of rRNA, and by using an advanced tree-building method that treated each paired site in the rRNA as an evolving character.  These methodological innovations, however, did not improve tree resolution, so the main benefit of our study is the incorporation of so many taxa (197) from across the Metazoa. 

In general, the findings matched those of past studies that used smaller subgroups of metazoans, recovering clades of the “new animal phylogeny” such as Ecdysozoa (the molting animals), Lophotrochozoa (annelids, molluscs, brachiopods, platyhelminths, etc.), Ambulacraria (hemichordates with echinoderms), and Pancrustacea (insects among the crustaceans).  Most of these clades, however, could only be recovered after eliminating some highly divergent, rapidly evolving rRNA sequences that otherwise disrupted the tree and went in unlikely positions: those of cephalopod molluscs, chaetognath arrowworms, of symphylan and pauropod myriapods, and tunicates.  Fortunately, these “rogue” sequences comprised only 5% of the 197 sequences.  Like other rRNA-based studies, we obtained evidence that the acoelomorph worms are not platyhelminths, as was traditionally believed, but instead diverged from the base of the bilaterian animals.  We also document the conserved nature of the rRNA genes of cnidarians (jellyfish, hydras, sea anemones, etc.), supporting cnidarians as the immediate sister group of Bilateria.  A new finding is that the extremely simple Placozoa joined with Cnidaria. 

Overall, our rRNA-based results agree with recent animal phylogenies that were calculated from multiple protein-coding genes and were likewise taken from a broad range of taxa across the Metazoa.  In conclusion, after the rogue sequences are removed, both rRNA- and protein-based phylogenies are now converging to support the same basic clades of the new animal phylogeny.