Maximum Likelihood phylogenetic tree derived from amino sequences of the DNA binding domain. A phylogenetic tree was constructed using the Maximum Likelihood (ML) method under Jones-Taylor-Thornton (JTT) substitution model with a gamma distribution of rates between sites (eight categories, parameter alpha, estimated by the program) using PHYML (v2.4.4)). Support values for the tree were obtained by bootstrapping a 100 replicates and are indicated above each branch. Branches under the bootstrap value of 50 were shown as polytomies. The same data set was also tested by Bayesian inference with a JTT amino acid replacement model + gamma rates. The trees were started randomly with four simultaneous Markov chains running for 5 million generations. Bayesian posterior probabilities (PPs) were calculated using a Markov chain Monte Carlo (MCMC) sampling approach implemented in MrBAYES v3.1.1, the PPs values are shown below each branch. Star indicates the node obtained by Bayesian inference which was different from that obtained by ML method. DpTR: water flea Daphnia pulex TR, LgTR: owl limpet Lottia gigantean TR, SeTRa: turbellarian Schmidtea mediterranea TRα, SeTRb: S. mediterranea TRβ, SjTRα: blood fluke Schistosoma japonium TR alpha, SjTRβ: S. japonium TR beta, SmTRα: blood fluke S. mansoni TR alpha, SmTRβ: S. mansoni TR beta, SpTR: sea urchin Strongylocentrotu purpuratus TR. The accession number of each sequence used for phylogenetic analysis can be found in Additional files 1 and 2.