Evolution of homeobox genes

Evolutionary tree showing total number of homeobox genes present in the genomes of selected animal species. The precise numbers are liable to change slightly with each release of a revised genome assembly; these data from HomeoDB2 accessed December 20113 1R, 2R, and 3R denote whole genome duplication events. (Animal diagrams by Tatiana Solovieva)

Deletion of a Pitx1 ‘pelvic enhancer’ in pelvic‐reduced sticklebacks. An enhancer region driving Pitx1 gene expression specifically in the pelvic region is located around 34 kb 5′ of the Pitx1 transcriptional start site (top line). A population of three‐spined sticklebacks from Salmon River has a complete pelvic region (shaded black) and the cis‐regulatory region is complete. Isolated freshwater populations (three examples shown) can have dramatically reduced pelvic regions, associated with deletion mutations covering or overlapping the characterized pelvic enhancer. (Based on data from Ref 102)

Schematic diagram showing segmental specialization in three crustacean species in relation to the the expression of Ubx protein, detected using an antibody recognizing Ubx and AbdA (blue domain). The six head segments shown are Oc, ocular; A1, first antennal; A2, second antennal, Mn, mandibular; Mx1, first maxillary; Mx2, second maxillary. Only the first five trunk segments are shown (T1–T5). Segments Mn, Mx1, and Mx2 usually bear feeding appendages, and trunk segments bear locomotory appendages. In Mysidium T1, and Homarus T1 and T2, trunk segments are modified as feeding appendages, in association with absence of Ubx protein expression. Mysidium T2 has an intermediate state. (Based on data from Ref 97)

Schematic diagram demonstrating correlation between the anterior expression boundary of the Hoxc6 gene (blue domain) and the cervical–thoracic boundary in different vertebrate species. The gene is expressed at earlier developmental stages, in embryonic somites, before formation of definitive vertebrae. Occipital vertebrae, which contribute to the base of the skull, are not shown. (Based on data from Ref 95)

Single Hox gene clusters in an insect (Drosophila melanogaster) and amphioxus (Branchiostoma floridae) are homologous to four gene clusters in human or mouse (Mus musculus). Color coding denotes division of Hox genes in ‘anterior’, ‘group 3’, ‘middle’, and ‘posterior’ groups. The group 3 gene in D. melanogaster has triplicated and diverged to give zen, zen2, and bcd. The Hox genes zen, zen2, bcd, and ftz have diverged in function and do not have homeotic roles.

Hypothetical role of Hox, ParaHox, and NK homeobox gene clusters in patterning of neural, gut, and mesodermal tissues in an early bilaterian animal. Anterior to the left.

Possible evolutionary history of the ANTP class homeobox genes, involving extensive tandem duplication to generate NK genes (red) and later ProtoHox genes (blue). Duplication of a hypothetical ProtoHox gene cluster (shown here as two genes, though the precise number is unresolved) gave distinct Hox and ParaHox gene clusters (blue and green, respectively).