Results of the maximum parsimony analysis for Drosophila and cnidarian homeobox-containing genes. Analysis was performed using the heuristic algorithm of PAUP 3.1.1 [Swofford, D.L. PAUP: Phylogenetic Analysis Using Parsimony, Version 3.1.1 (Computer program distributed by the Illinois Natural History Survey, Champaign, Illinois, 1993)] with TBR branch swapping for 500 randomly constructed initial trees. The analysis generated a single most parsimonious cladogram (length: 4644 steps; consistency index: 0.364; retention index: 0.465). The data set analyzed combined amino acid and nucleotide sequence for the homeobox region in a single matrix in a modification of the approach described in Agosti et al, 1996 [Agosti, D., Jacobs, D. & Desalle, R. On combining protein sequences and nucleic acid sequences in phylogenetic analysis: The homeobox protein case. Cladistics 12, 65-82 (1996)]. Because most of the cnidarian sequences showed substantial AT richness, third codon positions were not included in the analyses and changes in amino acids were given a weight of 3 times changes in nucleotides. Genes shown in blue, together with genes used as outgroups, were included in the additional analysis which focused on HOX genes. Sequence data for the majority of genes were obtained from GenBank. References for cnidarian sequences as follows:

Acropora formosa: Miles, A. & Miller, D.J. Genomes of diploblastic organisms contain homeoboxes: sequence of eveC, an even-skipped homologue from the cnidarian Acropora formosa. Proceedings of the Royal Society of London. Series B, Biological Sciences 248, 159-161 (1992).

Chlorohydra viridissima: Schummer, M., Scheurlen, I., Schaller, C. & Galliot, B. HOM/HOX homeobox genes are present in hydra (Chlorohydra viridissima) and are differentially expressed during regeneration. EMBO 11, 1815-1823 (1992).

Eleutheria dichotoma: Kuhn, K., Streit, B. & Schierwater, B. Homeobox genes in the cnidarian Eleutheria dichotoma: Evolutionary implications for the origin of Antennapedia-class (HOM-Hox) genes. Mol. Phyl. Evol. 6, 30-38 (1996).

Hydra littoralis: Sun, H., Rodin, A., Zhou, Y., Dickinson, D.P., Harper, D.E., Hewett-Emmett, D. & Li, W.-H. Evolution of paired domains: Isolation and sequencing of jellyfish and hydra Pax genes related to Pax-5 and Pax-6. Proc. Natl. Acad. Sci. USA. 94, 5156-5161 (1997).

Hydra vulgaris: Shenk, M.A., Bode, H.R. & Steele, R.E. Expression of Cnox-2, a HOM/HOX homeobox gene in hydra, is correlated with axial pattern formation. Development 117, 657-667 (1993).

Hydra vulgaris: Gauchat, D., Kreger, S., Holstein, T. & Galliot, B. prdl-a, a gene marker for hydra apical differentiation related to triploblastic paired-like head-specific genes. Development 125, 1637-1645 (1998).

Hydra magnipapillata: Naito, M., Ishiguro, H., Fijisawa, T. & Kurosawa, Y. Presence of eight distinct homeobox-containing genes in cnidarians. FEBS 333, 271-274 (1993).

Podocoryne carnea: Aerne, B.L., Baader, C.D. & Schmid, V. Life stage and tissue-specific expression of the homeobox gene cnox1-PC of the hydrozoan Podocoryne carnea. Developmental Biology 169, 547-556 (1995).

Unpublished sequence for the following genes was used: Hydractinia symbiolongicarpus Cnox-1 and Cnox-2; Podocoryne carnea Cnox-2 and Cnox-3; Hydra vulgaris Cnox-3,Manacle,Cnmsh and Cnotx.

The authors would like to thank several colleagues who kindly provided some of the unpublished sequences used in our analyses: Hans Bode, Alexey Leontovich, Kerstin Kuhn, Timothy McCord, Volker Schmid, Kerry Smith, and Xiaoming Zhang.