The homeobox gene system presents a unique model for experimental and
theoretical analyses of gene evolution. Homeobox genes play a role in
patterning the embryonic development of diverse organisms and as such
are likely to have been fundamental to the evolution of the specialize
d body plans of many animal species. The organization of Hox-genes in
chromosomal, clusters in many species implicates gene duplication as a
prominent mechanism in the evolution of this multigene family. I revi
ew here various theoretical analyses that have contributed to our unde
rstanding of the molecular evolution of this class of developmental co
ntrol genes. This article also illustrates relationships between theor
etical predictions and experimental studies and outlines future avenue
s for the evolutionary analysis of developmental systems.