Phylogenies of the gene families identified in our analysis for which more than three family members were present. (a) SP and KLF families; (b) Odd-like family; (c) Spalt family; (d) YY1 family; (e) Disco family; (f) IA-1 family; (g) Zep family; (h) Zic and Gli families; (i) Evi-1 family; (j) Snail family; (k) Ovo family; (l) Egr family. In each tree, the scale bar indicates a maximum likelihood branch length of 0.1 inferred substitutions per site and the numbers next to relevant branches are percentage quartet-puzzling support values. Genes and branches are color coded according to species: human genes are red, Drosophila genes are blue and C. elegans genes are green. Most trees are unrooted and built with members of only a single orthology group, as in only two cases could sequences from separate groups be confidently aligned. One of these exceptions is the SP and KLF families (a), which were analyzed together as their similar ZNF number and structure suggest relatively recent common ancestry. The other is the Zic and Gli families (h), which have a similar number and arrangement of C2H2 fingers. This tree also includes two 'orphan' Drosophila genes that have a similar finger arrangement. The phylogenetic analyses, with the exception of the KLF group, either failed to resolve relationships sufficiently to confirm or disprove orthology or showed that each group was descended from a single gene present in the common ancestor of humans, C. elegans and Drosophila. We therefore call these families 'orthology groups', implying that genes from different species within each family are orthologs. Consequently, genes from one species within a family are paralogs. For the KLF and SP genes, the tree topology shows monophyly of the SP genes and suggests that multiple KLF orthology groups may be present, although the poor resolution does not allow definition of these.