Figure 2

ANTP tree. Mnemiopsis homeodomains are in red. Arrows represent single genes or clades consisting entirely of Mnemiopsis sequences. Collapsed clades (triangles) represent clades with no Mnemiopsis representative. These clades have families represented in bold along with the phyla/subkingdom who have sequences represented in the collapsed clade (P = Protostomia; D = Deuterostomia; C = Cnidaria; T = Placozoa; A = Porifera). Support values shown are maximum likelihood (ML) bootstrap greater than 50%. Nodes with posterior probabilities generated by MrBayes greater than 50 are represented by a black dot and those clades with posterior probabilities greater than 90 are represented by a red dot. For visibility, trees were initially formatted in FigTree [53] as cladograms with decreasing ordered nodes and uniform branch lengths. They were later formatted by hand in Adobe Illustrator. Rooting of this tree is for display purposes only; branch lengths are presented uniformly, also for display purposes. Actual branch lengths can be viewed by opening the Newick-formatted tree file (Additional File 4), which also includes bootstrap and Bayesian support values, in a tree viewing/editing program such as FigTree [53]. Homeodomain names are prefixed with two letter species abbreviations as follows: Ml = Mnemiopsis leidyi; Aq = Amphimedon queenslandica (Porifera/demosponge); Ta = Trichoplax adhaerens (Placozoa); Nv = Nematostella vectensis (Cnidaria/starlet sea anemone); Dm = Drosophila melanogaster (Protostomia/fruitfly); Bf = Branchiostoma floridae (Deuterostomia/amphioxus); Hs = Homo sapiens (Deuterostomia/human). Other taxa codes either from collapsed clades of this tree or in other trees: Hv = Hydra vulgaris (Cnidaria/hydrozoan); Pd = Platynereis dumerilii (Protostomia/annelid worm); Am = Apis mellifera (Protostomia/honey bee); Ps = Phascolion strombus (Protostomia/sipunculan worm); Sm = Strigamia maritima (Protostomia/centipede); Mb = Monosiga brevicollis (choanoflagellate). Mnemiopsis sequences are shown in red; human and other deuterostome sequences are shown in blue; Drosophila and other protostome sequences are shown in green; cnidarian sequences are shown in brown; Trichoplax sequences are shown in purple; and Amphimedon sequences are in orange.