Figure 2

Phylogenetic analysis of Irx and Mkx genes. The represented tree is a maximum-likelihood tree, which has been rooted using the mouse TALE homeodomain TGIF as an outgroup. This tree is based on a multiple alignment that includes the homeodomain plus a few flanking aminoacids of most of the retrieved Irx and Mkx. Similar relationships (with similar statistical supports) were found when we used the entire set of Mkx and Irx sequences. The Irx and Mkx groups are indicated in blue and the associated numbers are their statistical support values obtained with different methods of phylogenetic reconstruction: first number is the bootstrap support in maximum-likelihood analysis (500 bootstrap replicates); second number is the posterior probabilities in Bayesian inference-based analysis; third number is the bootstrap support in neighbour-joining analysis (10,000 bootstrap replicates); fourth number is the bootstrap support in maximum-parsimony analysis (1,000 bootstrap replicates). The asterisk associated with the support in the neighbour-joining analysis indicates that in the neighbour-joining tree, the strongly supported Irx group does not include the sponge genes which are found as outgroup to both Irx and Mkx proteins. Statistical support in the maximum-likelihood analysis for some other internal branches is indicated in black. Only statistical support values >50% are shown except for a few cases.