The system of Signal Transduction and GRNs is incredibly flexible. Even though there are conserved units (like kernels and signal transduction pathways) the way these conserved units are connected to each other can be diverse both within a developing embryo and between different species. As new interactions evolve, this can lead to novelty. For example, the yellow box in Figure 2 contains a GRN battery that is used in skeleton formation across echinoderm classes. In the sea urchin shown this has been reused to make a special larval skeleton derived from a group of cells called the micromeres1,8 Loss of features can also be correlated with changes to connections between the genes in GRNs. For example, the gene pitx1 is a switch for skeleton patterning (it is a transcription factor that controls a battery that patterns mesodermal tissues)9. Loss of a cis regulatory element that turns it on in pelvic regions leads to a reduced pelvis. This mutation is common in freshwater fish populations, where a smaller pelvis may be beneficial, but not in marine fish populations, where a more robust pelvis may be beneficial10 (Figure 5).
Figure 6: Cis-regulatory regions upstream of the pitx1 gene regulate the expression pattern of the gene and affect the size/shape of the pelvis. Figure by Amanda Lo and Ajna Rivera
There are many more examples of GRN evolution leading to changes in body plan, and we will cover some of them later. But I would like to mention one final example that you are already familiar with. The Hox genes are an animal synapomorphy, that is they are unique to the animal evolutionary lineage and found in most animals. In animals where Hox genes have been genetically examined, Hox genes are often involved in the same process - early regionalization along the A/P axis. Different sets of Hox genes are turned on at different locations along the A/P axis of the animal body. Interestingly, this appears to be an ancient conserved kernel for body patterning since many diverse species exhibit the same patterning (Figure 7).
Figure 7: Hox genes and their expression patterns in Cnidaria and Bilateria. From DuBuc et al, 2018 published under a CC BY 4.0 license