Tree Life

Vol 452 | 10 April 2008 | doi:10.1038/nature06614

LETTERS
Broad phylogenomic sampling improves resolution of the animal tree of life
Casey W. Dunn1{, Andreas Hejnol1, David Q. Matus1, Kevin Pang1, William E. Browne1, Stephen A. Smith2, Elaine Seaver1, Greg W. Rouse3, Matthias Obst4, Gregory D. Edgecombe5, Martin V. Sørensen6, Steven H. D. Haddock7, Andreas Schmidt-Rhaesa8, Akiko Okusu9,Reinhardt Møbjerg Kristensen10, Ward C. Wheeler11, Mark Q. Martindale1 & Gonzalo Giribet12,13

Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data1,2. These new hypotheses include a clade of moulting animals (Ecdysozoa)3 and the close relationship of the lophophorates tomolluscs and annelids (Lophotrochozoa)4. Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report atotal of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standingissues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods5), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (includingsipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineagesremain recalcitrant to placement on the tree. Expressed sequence tags (ESTs) provide opportunities to sample diverse genes from a large number of taxa6. Several recent phylogenomic studies, based largely on EST data, analysed matrices containing more than 140 genes from up to 34 metazoans (multicellular animals)7–9. However, the included species were not well sampled across extant metazoandiversity. These analyses also relied on either ribosomal proteins or a list of target genes identified from a small (1,152 ESTs) choanoflagellate data set10, limiting the possibilities of

EST studies to inform gene selection and homology assignment. Rather than look for predefined sets of genes in our data, we present an explicit procedure for gene selection (see Methods and Supplementary Fig. 2).Our complete matrix includes data from 77 taxa (of which 71 are metazoans) and 150 genes. On average, taxa in our matrix include 50.9% of the 150 genes, and overall matrix completeness is 44.5%. Maximum likelihood (WAG model of sequence evolution; Figs 1 and 2) and bayesian (CAT11 and WAG models of sequence evolution; Fig. 2) analyses of our matrix support the major groups of the ‘new animalphylogeny’2. These groups have also been supported by other EST-based analyses9, but not by phylogenomic studies that consider a small number of animal taxa12. Primary analyses of the 77-taxon matrix recover Metazoa, Bilateria and Protostomia with strong bootstrap support (.90%). This is an improvement compared to some previous phylogenomic studies that did not recover Protostomia, which in part led...