Figure 4

Evidence for orthology between cyclostome EmxB and gnathostome Emx2. (a) Synteny conservation between the genomic regions containing Emx2 of gnathostomes and EmxB of sea lamprey. Assignment of gene names in this figure was based on orthology information in Ensembl except the one in a parenthesis (“Slc18a2”) which was assigned by using BLASTP. (b) Molecular phylogeny of vertebrates Pdzd8 genes, included in the Emx-containing genomic regions in (a). This ML tree was inferred using 600 amino acid sites in the multiple alignment in Additional file 10, assuming the JTT model with amino acid frequencies taken into account (JTT + Γ₄ + F model) (shape parameter α = 1.17). The numbers at nodes indicate bootstrap probabilities with 100 replicates for the ML and NJ methods, in order.