Magazine R575 Metazoa. Each of these three (100% posterior probability), Correspondences datasets is broadly sampled as well as Ecdysozoa (88%) across the Metazoa. We have and Lophotrochozoa (100%). also sequenced ~ 5000 ESTs Chaetognaths are placed as Broad taxon and from the pelagic chaetognath sister to lophotrochozoans Flaccisagitta enflata, recovering (100%) (Figure 1A). gene sampling 72 of the genes used by Philippe Bayesian analyses of the indicate that et al. [4]. Preliminary analyses of 72 genes in the EST dataset SSU and LSU ribosomal RNAs (11,650 amino acids) positioned chaetognaths are showed chaetognath sequences the chaetognaths as sister clustering with taxa that also to the lophotrochozoan taxa protostomes show long phylogenetic branches (annelids and molluscs) and a higher than average GC (Figure 1B; Supplemental data), David Q. Matus1, Richard R. content (see Supplemental data while maximum likelihood Copley2, Casey W. Dunn1, published with this article online). analyses placed them within Andreas Hejnol1, Heather In order to address the possibility the protostomes but did not Eccleston3, Kenneth M. that this grouping was an artifact resolve their relationship to other Halanych3, Mark Q. Martindale1, of GC content, we recoded all protostome taxa (Supplemental and Maximilian J. Telford4,* nucleotides as purines (A,G = R) data). Most features of this tree and pyrimidines (C,T/U = Y). were consistent with the ‘new’ Despite advances in phylogenetic Maximum likelihood and Bayesian metazoan phylogeny [4,7–9], methods, there are still a number analyses of this recoded dataset with the notable exception that of enigmatic phyla whose grouped the chaetognaths the platyhelminths grouped with affinities remain poorly resolved. with the priapulids within the nematodes. To eliminate long One of the most recalcitrant Ecdysozoa (Supplemental branch attraction artefacts, we of these is a group of small data). However, with priapulids analyzed subsets of taxa to predatory marine invertebrates, excluded, chaetognaths grouped determine the effects of taxon the chaetognaths (arrow worms). with the Lophotrochozoa (100% sampling (Supplemental data). Resolution of the phylogenetic posterior probability), without Regardless of the taxa removed position of the chaetognaths resolving their position within the (nematodes, platyhelminths or is key for reconstructing the group (Supplemental data). The tardigrades) the chaetognaths evolutionary history of some association with the Ecdysozoa, remained as sister to annelids of the most fundamental therefore, depends on a single and molluscs with varying features of animals, including taxon and is not likely to reflect a degrees of support in Bayesian those that have been used to general affinity for the group. analyses and as sister to delineate two major clades of Furthermore, we analyzed the Ecdysozoa (arthropods, animals — the protostomes and two complete chaetognath nematodes and tardigrades) deuterostomes. An affiliation of mitochondrial genomes in with weak bootstrap support in chaetognaths to deuterostomes combination that previously were likelihood analyses (Figure 1B; was inferred from a number analyzed independently with also see Supplemental data). of shared embryological and differing results [5,6]. Bayesian Topological tests on all four morphological features including analysis of the nucleotide datasets did not reject the radial, indeterminate cleavage, matrix places chaetognaths hypotheses that chaetognaths a posterior position of the within the Lophotrochozoa form a clade with ecdysozoans. blastopore (deuterostomy), allied to molluscs, and Bayesian Only the Tropomyosin dataset enterocoelous coelom formation, analysis of the amino acid matrix rejected the positioning of and a tripartite adult body places them as sister to the chaetognaths as sister to the plan with a post-anal tail [1,2]. Lophotrochozoa (Supplemental protostomes as significantly Various other features (e.g., a data). Maximum likelihood worse. (Shimodaira-Hasegawa ventrally positioned nervous analyses of nucleotide and test using RELL bootstrapping; system, ecdysozoan-like spines, amino acid datasets support the Supplemental data). and a lack of circular body wall hypothesis that chaetognaths All of our analyses indicate muscle) have been interpreted as are sister to lophotrochozoans that chaetognaths are evidence of a protostome albeit incongruously allied with protostomes, consistent with affinity [3]. the long branched arthropod other recent studies [5,6,10] and Here, we analyse the Ornithoctonus huwena using the accompanying paper [11]. phylogenetic position of the nucleotide data (Supplemental This has implications for our chaetognaths using existing data). Bayesian and likelihood understanding of the evolution datasets, i.e. small and large analyses of tropomyosin from of morphological characters and subunit nuclear ribosomal RNAs 56 taxa (Supplemental data) for the reconstruction of the last (SSU and LSU), and complete show unequivocal support for common ancestor of protostomes mitochondrial genomes. We the new metazoan phylogeny and deuterostomes. The early also report a new dataset from within the Bilateria, recovering a development of chaetognaths the tropomyosin gene of many monophyletic Protostomia clade resembles a radial cleavage Current Biology Vol 16 No 15 R576 References A 100 B 91 Arthropoda (15) 1. Doncaster, L. (1902). On the 71 73 development of Sagitta, with notes on 100 88 100 Nematoda (3) the anatomy of the adult. Q.J Microsc. 70 100 Arthropoda (10) Sci. 46, 351–398. Tardigrada (1) 93 100 2. Hertwig, O. (1880). Uber die 83 Nematoda Entwicklungsgeschichte der Sagitten. 100 Jena Z. Med. 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Chætognath of the spiralian lophotrochozoans within this group remains phylogenomics: a protostome