Changes in the spatial regulation of toolkit genes and the genes they regulate are associated with morphological divergence.
A vast body of data has accumulated that has linked differences in where toolkit genes are expressed, or where the genes they regulate are expressed, with morphological differences between animals at various taxonomic levels. Most studies have analyzed situations in which the spatial location of a developmental process (for example, the making of a limb, the formation of a pigmentation pattern, the development of epithelial appendages, etc.) has been altered. The classical term for such spatial changes in development is heterotopy (changes in the timing of a process are known as heterochrony). The close correspondence between heterotopic shifts in gene expression, development, and morphology, combined with the known roles of these genes in model taxa, have provided compelling evidence that changes in morphology generally result from changes in the spatiotemporal regulation of gene expression during development.
Explanations for the evolution of anatomy have thus focused on the genetic and molecular mechanisms underlying the evolution of spatial gene regulation. And the keys to understanding spatial gene regulation are the architectures of gene-regulatory regions and transcriptional networks.
Sean B. Carroll. Cell 134, July 11, 2008.