Fig. 3

RRTs of the gnathostome Hox gene sequences. a Evolutionary relationship of the gnathostome species used in the RRTs of the Hox genes. b Summary of the RRTs conducted on the Hox gene nucleotide sequences. For most of the Hox genes, RRTs were performed using Banna caecilian, Western clawed frog, Puerto Rican worm lizard/Chinese softshell turtle and human as the ingroups and Indonesian coelacanth as the outgroup. RRTs of HoxC1 were carried out using elephant shark as the outgroup and caecilian, African lungfish, eel and zebrafish as the ingroups to replace the species that do not have HoxC1 gene. For HoxC3, the ingroups included caecilian, frog, Alpine stream salamander and African lungfish and the outgroup was Indonesian coelacanth. Results of RRTs for each gene are shown in a Hasse diagram, in which the slower-evolving genes are placed below the faster-evolving ones, with statistical significance denoted as a solid line (p ≤ 0.01, high significant) or a dotted line (0.01 < p ≤ 0.05, significant). c Summary of the significant RRTs among Banna caecilian, Western clawed frog, Puerto Rican worm lizard and human. For each pair of species, the significant RRTs are denoted by arrows pointing to the slower-evolving one. The number of highly significant (significant) tests for each Hox cluster is indicated on the side of the arrow