1. Kewalo Marine Laboratory, PBRC, University of Hawaii, 41 Ahui Street, Honolulu, Hawaii 96813, USA
2. Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, Connecticut 06520, USA
3. Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive 0202, La Jolla, California 92093, USA
4. Kristineberg Marine Research Station, Kristineberg 566, 450 34 Fiskebäckskil, Sweden
5. Department of Palaeontology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
6. Ancient DNA and Evolution Group, Biological Institute, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
7. Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, California 95039, USA
8. Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
9. Biology Department, Simmons College, The Fenway, Boston, Massachusetts 02115, USA
10. Zoological Museum, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
11. Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024, USA
12. Department of Organismic and Evolutionary Biology,
13. Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138, USA
14. Present address: Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, Rhode Island 02912, USA.

Correspondence to: Casey W. Dunn^1,14 Correspondence and requests for materials should be addressed to C.W.D. (Email: casey_dunn@brown.edu).

Abstract

Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data^{1, 2}. These new hypotheses include a clade of moulting animals (Ecdysozoa)³ and the close relationship of the lophophorates to molluscs 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 a total 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-standing issues 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 (including sipunculans 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 lineages remain recalcitrant to placement on the tree.