Phylogenetic relationships of pufferfish Hox clusters. Neighbor-joining trees are based on amino acid sequences as described (Amores etal. 1998). (A) Paralog group 13, exon 1, and exon 2. The tree is as expected if Hox cluster duplication occurred before the divergence of pufferfish and zebrafish lineages. (B) Paralog group 13, exon 2 only (due to limited sequence availability). The tree shows that Hoxa13c is the sister group to Hoxa13a. (C) Hoxa11a of pufferfish and zebrafish group as sisters, but Hoxa11b orthologs do not. (D) Hoxa9 tree strongly supports duplication before lineage divergence, and the close similarity of the Hoxaa and Hoxac clusters. (E,F) The Hoxb1 and paralog group-5 trees support duplication before lineage divergence. (G) The paralog group-4 tree shows rapid evolution of Hoxd4b. (H) The Hoxb6 tree supports duplication before lineage divergence. Alignments and accession numbers are available as Supplemental material. Numbers are bootstrap values per 1000 runs. (Cca) Carassius carassius, crucian carp; (Dae) Danio aequipinnatus, giantdanio; (Bfl) Branchiostoma floridae, amphioxus; (Dre) Danio rerio, zebrafish; (Gga) Gallus gallus, chicken; (Hfr) Heterodontus francisci, horned shark; (Hsa) Homo sapiens, human; (Mmu) Mus musculus mouse; (Msa) Morone saxatilis, striped bass; (Ola) Oryzias latipes, medaka; (Pma) Petromyzon marinus, lamprey; (Pol) Paralichthys olivaceus, Japanese flounder; (Sne) Spheroides nephalus, Southern pufferfish; (Tru) Takifugu rubripes, Japanese pufferfish.