An even ‘‘newer’’ animal phylogeny Rob DeSalle 1 * and Bernd Schierwater 2 Summary Metazoa are one of the great monophyletic groups of organisms. They comprise several major groups of organisms readily recognizable based on their anatomy. These major groups include the Bilateria (animals with bilateral symmetry), Cnidaria (jellyfish, corals and other closely related animals), Porifera (sponges), Cteno- phores (comb jellies) and a phylum currently made up of a single species, the Placozoa. Attempts to systematize the relationships of these major groups as well as to determine relationships within the groups have been made for nearly two centuries. Many of the attempts have led to frustration, because of a lack of resolution between and within groups. Other attempts have led to ‘‘a new animal phylogeny’’. Now, a study by Dunn et al., (1) using the expresssed sequence tag (EST) approach to obtain- ing high-throughput large phylogenetic matrices, presents an ‘‘even newer’’ animal phylogeny. There are two major aspects of this study that should be of interest to the general biological community. First, the methods used by the authors to generate their phylogenetic hypotheses call for close examination. Second, the relationships of animal taxa in their resultant trees also prompt further discussion. BioEssays 30:1043–1047, 2008. ß 2008 Wiley Periodicals, Inc. Introduction How animals are related to each other has been a major pre- occupation of biologists for centuries. Some bold ideas about animal relationships have populated the literature, caused controversy and, in at least one case,—Cuvier and Geoffroy— destroyed a collegial and personal relationship. Most early anatomical systems of classification at this level suffered because of difficulties in establishing homology of anatomical parts. Two historical examples of this problem involve (1) the long-standing issue of establishing homology of dorsal– ventral polarity (an argument that caused the main riff between Cuvier and Geoffroy and resulted in their great confrontation in Paris that started in 1830; (2) and (2) the longstanding doubts about the existence of a monophyletic Protostomia (Box 1). Anatomy has had and continues to have a predominant role in classifying animals into higher groups; for example, the three major animals groups—Bilateria, Cnidaria, Porifera— can easily be distinguished from each other using morphology. The relationships of several enigmatic groups of animals within these phyla causes much more confusion. In addition, the relationships of the three major groups to each other, and the placement of two other important taxa (Ctenophora and Placozoa) have caused problems with this part of the tree of life. Molecules to the rescue? It was only 20 years ago that molecular analysis claimed to address the major problems in animal phylogeny. At this time, microbiologists had started to successfully unravel the relationships of the difficult to decipher Bacteria and Archaea using 16S rRNA sequences as characters for systematic analysis. In line with these studies in microbial systematics, Field et al., (5) used eukaryotic18S rRNA genes as a source of characters from several metazoan taxa, and proposed one of the first molecular hypotheses for this part of the tree of life. This landmark paper is remembered more for its prophetic focus on the problems associated with animal phylogenetics, than for the overall phylogenetic hypothesis proffered by the analysis. The prophecies of the Field et al., (5) paper include pointing to difficulties in determining robustness of inference. Bootstrapping was only beginning to be developed for phylogenetic analysis at the time, and both jackknifing and Bayesian phylogenetic inference were chocolate bars in some systematists’ back pockets. Another issue prophesized by Field et al., (5) was a dutiful concern for how to treat molecular information in light of morphological patterns. The authors of this paper also pointed to varying phylogenetic incongruence as a result of the choice of phylogenetic method (at that time parsimony versus distance). Finally, the paper was also rather clairvoyant with respect to some of the major controversial hypotheses about animals and added to the number of hypotheses for this part of the tree of life. The Field et al., (5) paper predated high-throughput sequencing techniques, sophisticated likelihood analyses and hence a strong under- standing of long branch attraction, data combination tech- niques, the impact of taxon sampling and several other 1 American Museum of Natural History, New York, Sackler Institute for Comparative Genomics, NY. 2 ITZ, Ecology & Evolution, TiHo Hannover, Bu ¨nteweg Germany. *Correspondence to: Rob DeSalle, American Museum of Natural History, New York, Sackler Institute for Comparative Genomics, 79 St at Central Park West, New York, NY 10024. E-mail: desalle@amnh.org DOI 10.1002/bies.20842 Published online in Wiley InterScience (www.interscience.wiley.com). BioEssays 30:1043–1047, ß 2008 Wiley Periodicals, Inc. BioEssays 30.11–12 1043 What the papers say