Species throughout the animal kingdom share not only housekeeping but also
many key regulatory genes. Nonetheless, species differ from one another dev
elopmentally and thus, also morphologically. One of the general aims of com
parative developmental genetics is to understand how similar molecules can
generate the known diversity of biological form. Here, we argue that gene f
unction can change in different ways during the evolution of developmental
processes. Genes can be recruited to serve completely new functions in a ne
w regulatory linkage (co-option), they can change their molecular specifici
ty while remaining in the original (homologous) developmental program and c
an, at the same time, retain other functions. We describe evidence for such
evolutionary patterns based on the comparison of loss-of-function mutation
s of homologous genes of the two free-living nematodes Caenorhabditis elega
ns and Pristionchus pacificus. Ultimately, it is the interplay of conservat
ion and change of the specificity of genes and genetic networks that genera
tes developmental novelty over evolutionary time.