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. Author manuscript; available in PMC: 2009 Jan 15.
Published in final edited form as: Dev Biol. 2007 Sep 26;313(2):501–518. doi: 10.1016/j.ydbio.2007.09.032

Figure 2. Phylogenetic analyses of hint/intein containing genes.

Figure 2

Both Bayesian and Maximum Likelihood analyses were conducted utilizing MrBayes 3.1.2 (Ronquist 2003), Phyml (Guindon et al. 2003), and RAxML v.2.3.2 (Stamatakis, 2006) utilizing an amino acid alignment of hint/intein-containing genes from metazoan and non-metazoan representatives. The three Nematostella hint-only containing genes (Hint1−3) (shown in red) form a monophyletic group in Bayesian analyses. The two true Nematostella (Nv) hedgehog genes (shown in red) do not show a sister group relationship as they do in analyses of the hedge and hint domains together (see SF6). NvHh1 is weakly supported as the sister group to vertebrate hh genes (shown in green (sonic), pink (Indian) and blue (desert)) while NvHh2 forms a polytomy with other hint-containing genes. All nematode hint-only containing genes (shown in light blue) from a monophyletic group sister to the true hedgehog gene from the nematode Xiphinema index (M. Blaxter, pers. comm.). The five hint-only genes from the demosponge, Amphimedon queenslandica (shown in orange) form a monophyletic group as well. Numbers above branches indicate Bayesian posterior probabilities while numbers below indicate ML bootstrap support. Additional details of phylogenetic analyses and nexus alignments are available in the supplemental information (SF2−7).