Fig. 3.

Maximum likelihood phylogeny of bilaterian MRFs. Major branches defining certain gene types, (e.g., the urochordate MRFs) are labeled with support values from three phylogenetic methods: ML (% 1,000 bootstraps)/BI (posterior probability)/NJ (% 1,000 bootstraps); values are represented by dashes when a certain topology was not present in that phylogeny. The tree is rooted on the branch separating the chordates from other bilaterians. The dotted line and corresponding support values represent the uncertainty of the placement of the urochordate sequences with support in ML and BI (44/0.79/–) and NJ (–/–/31). Colored boxes indicate gene types. The scale bar represents substitutions per site for the consensus ML tree (though not for the ambiguous urochordate branch; its node was manually drawn).