Walter Jakob Gehring discovered the homeobox, a DNA segment found in a specific cluster of genes that determine the body plan of animals, plants, and fungi. Gehring identified the homeobox in 1983, with the help of colleagues while isolating the Antennapedia (Antp) gene in fruit flies (Drosophila) at the University of Basel in Basel, Switzerland. Hox genes, a family of genes that have the homeobox, determine the head-to-tail (anterior-posterior) body axis of both vertebrates and invertebrates. Gehring also identified the homeobox-containing Pax-6 gene as the master control gene in eye development of Drosophila, the same gene that, when mutated or absent in humans, leads to aniridia, or lack of the iris, in humans. Gehring's work with the homeobox suggested to biologists that widely different species share a similar and evolutionarily conserved genetic pathway that controls the development of overall body plans, from fruit flies to humans.

Edwin Stephen Goodrich studied the structures of animals in England during the nineteenth and twentieth centuries. Goodrich studied how animals develop to identify their parts and to establish the evolutionary relationships between different species. Goodrich established that body structures can shift their positions relative to an organism's body during evolution, and he hypothesized that body structures can share ancestry (homology) between organisms of different species, even without identical body placement. Goodrich claimed that any given characteristic of an organism results from both genetic and external sources.

In the early 2000s, Manjong Han, Xiaodang Yang, Jennifer Farrington, and Ken Muneoka investigated how genes and proteins in fetal mice (Mus musculus) influenced those fetal mice to regenerate severed toes at Tulane University in New Orleans, Louisiana. The group used hind limbs from mice to show how the gene Msx1 (Homeobox 7) functions in regenerating amputated digits. The researchers showed that in the process of regenerating digit tips, Msx1 genes make products that regulate or influence other genes, such as the Bone Morphogenetic Protein 4 gene (BMP4 gene), to produce proteins, such as the BMP4 proteins. The researchers also showed that BMP4 proteins, which are produced from the BMP4 gene, function in tissues during the process of limb development. Furthermore, while Msx1 genes regulate other genes during the process of regeneration, they don't produce proteins otherwise needed to organize cells in the regeneration of digit tissues. The group published their results in 2003 as Digit Regeneration Is Regulated by Msx1 and BMP4 in Fetal Mice.

In 1995, researchers Ann Burke, Craig Nelson, Bruce Morgan, and Cliff Tabin in the US studied the genes that regulate the construction of vertebra in developing chick and mouse embryos, they showed similar patterns of gene regulation across both species, and they concluded that those patterns were inherited from an ancestor common to all vertebrate animals. The group analyzed the head-to-tail (anterior-posterior) axial development of vertebrates, as the anterior-posterior axis showed variation between species over the course of evolutionary time. Along those axes, they showed where Hox genes produced RNAs. Hox genes have the homeobox, a portion of DNA contributes to the generation of the body plans of animals, plants, and fungi. In the 1995 study, the researchers compared the expression patterns of Hox genes across the chick and mouse embryos, showing where the patterns were similar and where they differed. Based on those comparisons, they argued that Hox genes were present in the ancestors of tetrapods and fishes, and that Hox genes function in the segmentation of the anterior-posterior vertebrate axis in both chick and mouse embryos.

In 2012, a team of scientists across the US conducted an experiment to find the mechanism that allowed a group of flatworms, planarians, to regenerate any body part. The group included Danielle Wenemoser, Sylvain Lapan, Alex Wilkinson, George Bell, and Peter Reddien. They aimed to identify genes that are expressed by planarians in response to wounds that initiated a regenerative mechanism. The researchers determined several genes as important for tissue regeneration. The investigation helped scientists explain how regeneration is initiated and describe the overall regenerative mechanism of whole organisms.