Supplementary Table S1 PCR Primers for COI Amplification. F, Forward Primer; F Int, Forward

Supplementary Table S1 PCR primers for COI amplification. F, forward primer; F int, forward primer for 3'-half; R, reverse primer; R int, reverse primer for 5' half

Supplementary Table S2 Overview of molecular dataset and GenBank accession numbers for new sequences. Previously published sequences indicated by "X". If not stated otherwise, sequences from Dohrmann et al. (2008, 2009). *, fragments did not overlap, leaving an internal gap.; –, missing data. Previously unsampled species in bold

aCollins (1998); bMedina et al. (2001); cHaen et al. (2007); dBorchiellini et al. (2001); eRosengarten et al. (2008); f "Lophocalyx n. sp." in Dohrmann et al. (2008, 2009); this species was recently described (Janussen & Reiswig, 2009)

Supplementary Table S2 References

Borchiellini, C., M. Manuel, E. Alivon, N. Boury-Esnault, J. Vacelet & Y. Le Parco, 2001. Sponge paraphyly and the origin of Metazoa. Journal of Evolutionary Biology 14: 171–179.

Collins, A. G., 1998. Evaluating multiple alternative hypotheses for the origin of Bilateria: an analysis of 18S rRNA molecular evidence. Proceedings of the National Academy of Sciences of the United States of America 95: 15458–15463.

Haen, K. M., B. F. Lang, S. A. Pomponi & D. V. Lavrov, 2007. Glass sponges and bilaterian animals share derived mitochondrial genomic features: a common ancestry or parallel evolution? Molecular Biology and Evolution 24: 1518–1527.

Janussen, D. & H. M. Reiswig, 2009. Hexactinellida (Porifera) from the ANDEEP III expedition to the Weddell Sea, Antarctica. Zootaxa 2136:1–20.

Medina, M., A. G. Collins, J. D. Silberman & M. L. Sogin, 2001. Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proceedings of the National Academy of Sciences of the United States of America 98: 9707–9712.

Rosengarten, R. D., E. A. Sperling, M. A. Moreno, S. P. Leys & S. L. Dellaporta, 2008. The mitochondrial genome of the hexactinellid sponge Aphrocallistes vastus: evidence for programmed translational frameshifting. BMC Genomics 9: 33.