The discovery of the striking positional conservation between the Ante
nnapedia and Bithorax homeotic gene complexes (ANT-C and BX-C) in Dros
ophila melanogaster and the murine Hox and human HOX clusters has had
a substantial impact on our understanding of the evolution of developm
ent and its genetic regulation. Structural differences do exist among
the mammalian Hox complexes and the ANT-C in D. melanogaster. To gain
further insight into the evolutionary changes among these complexes, t
he ANT-C was cloned in the closely related species, Drosophila pseudoo
bscura. The overall structure of the ANT-C in D. pseudoobscura is high
ly similar to its D. melanogaster counterpart; however, two difference
s in the organization of the ANT-C have been identified. First, the z2
gene, a member of the ANT-C in D. melanogaster, is not present in the
D. pseudoobscura ANT-C and is possibly absent from the D. pseudoobscu
ra genome. Second, the orientation of the Deformed gene is inverted in
D. pseudoobscura, providing it with a 5' to 3' direction of transcrip
tion identical to the remaining ANT-C homeobox genes with the exceptio
n of fushi tarazu. These differences demonstrate that subtle changes c
an occur in ANT-C structure during relatively short periods of evoluti
onary divergence, although the fundamental organization of the complex
is conserved. These observations and others suggest that the complex
is not absolutely rigid but that selective pressures have maintained t
his organization of genes for some functional reason that remains elus
ive.