An Example of Functional Divergence in Hox6 Paralogs. The phylogeny of the genes is shown on the left with the location of the cluster duplication indicated with an open circle and speciation events indicated with a closed circle. Post cluster-duplication branches (PCD) and post speciation branches (PS) are highlighted blue and gray, respectively. These branch types were used in the calculation of ωPCD and ωPS in two ratio analyses for all paralog groups. The amino acid sequence of Hox6 genes from human (Hsa), chicken (Gga), frog (Xtr), coelacanth (Lme) and shark (Hfr) are shown on the left with divergent sites highlighted in red. Below the alignment sites are identified as type-I (1), type-II (2) or both (3). Amino acid substitutions are classified as conservative (C), moderate (M) or radical (R).