Phylogenetic analyses of Sox HMG domains. The tree was computed using Maximum Likelihood (ML) from an amino-acid alignment of complete HMG domain sequences (79 amino-acids; except for CheSox1, PpiSox2, PpiSox3, PpiSox12, EmuSox1, EmuSox2 and EmuSox3, for which only the 68 C-terminal amino-acids were included). The tree likelihood was logL = -8933.874657. Numbers associated with the branches correspond to ML bootstrap proportions (100 replicates)/NJ bootstrap values (1.000 replicates)/Bayesian posterior probabilities. Support values below 50% are indicated by a dash; maximal support values by a star. Abbreviated species names as follows: Acropora millepora, Ami; Amphimedon queenslandica, Aqu; Caenorhabditis elegans, Cel; Ciona intestinalis, Cin; Clytia hemisphaerica, Che; Drosophila melanogaster, Dme; Ephydatia muelleri, Emu; Gallus domesticus, Gdo; Globodera rostochiensis, Gro; Hydra magnipapillata, Hma; Homo sapiens, HSA; Monosiga brevicollis, Mbr; Nematostella vectensis, Nve; Oncorhynchus mykis, Omy; Pleurobrachia pileus, Ppi; Neurospora crassa, Ncr; Saccharomyces cerevisiae, Sce. Genes from Clytia hemisphaerica investigated in the present expression study are in red. Other Sox cnidarian sequences are indicated in pink; sponge sequences are in green, ctenophore sequences in blue and bilaterian sequences in black. The main Sox groups are indicated on the right. Unclassified sequences are highlighted using grey boxes. Symbols were used to label genes associated with either undifferentiated state and proliferation (circle) or cell differentiation (star) in three animal taxa: mammals [2, 3, 48, 57], the ctenophore P. pileus  and C. hemisphaerica (this study).