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Figure 3 | BMC Evolutionary Biology

Figure 3

From: Evolution of a novel subfamily of nuclear receptors with members that each contain two DNA binding domains

Figure 3

Maximum Likelihood phylogenetic tree derived from sequences of DNA binding domains. Amino acid sequences were aligned with ClustalW. Phylogenetic relationships were examined by 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 threshold value of 27 (this value was set to support subfamily II as a monophyletic group) were shown as polytomies. The same data set was also tested by Bayesian inference. 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 or after the ML bootstrapping value separated by a slash. Star indicates the node obtained form by Bayesian inference which was different from that obtained by ML method. The accession number of each sequence used for the phylogenetic analysis can be found in additional file 2 and 3.

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