Worm proteins with two bHLH domains. A rooted NJ tree is shown that depicts the phylogenetic relationships of the five worm proteins with two bHLH domains. Mouse genes representative of some of the animal families have been included in this analysis. Rooting is as in Figure 1. Numbers above branches indicate per cent support in bootstrap analyses (1,000 replicates). As in Figure 1, the rooting should be considered arbitrary. Branch lengths are proportional to distance between sequences. Mm, Mus musculus; Ce, Caenorhabditis elegans. The sequences of the first bHLH of each worm proteins are shown in blue, the second in red. Both form monophyletic groups with high bootstrap values, indicating that these proteins originate from an ancestral protein that already had two bHLH domains. There is, furthermore, a weaker support (40% bootstraps) for an association of the two bHLH domains into a monophyletic group (not shown in the figure, as only nodes with 50% or more support are shown), suggesting that the ancestral protein may have acquired its two bHLH domains through tandem duplication rather than by association of unrelated bHLH domains.