tation experiments (Kieny et al., 1972), solely because they arose along the dorsal midline in different compartments expressing different Hox genes. Similarly, Drosophila has a single developmental process for forming appendages; in the thorax it produces a leg, but in the head it produces biting mouthparts, because of different regulators introduced by different selector genes (Carroll et al., 1995; Lovegrove et al., 2006). Likewise, the forelimbs and hind limbs of vertebrates differ because of compartment-specific regulatory differences (Hox and Tbx genes).
Compartmentation facilitates the generation of phenotypic variation; that in one compartment does not constrain that in another (Schlosser and Wagner, 2004). Regulatory specification occurs independently and in parallel in different compartments. Also, we think that the compartment map deconstrains development preceding the phylotypic stage, when it first appears. The single-celled egg, we suggest, develops the compartment map by a robust adaptable process requiring little regulatory input. Thereby, the egg is freed to evolve fitness-enhancing diversifications of size, shape, nutrient provision, and gastrulation, as happened repeatedly in chordates and arthropods. After the phylotypic stage, as noted previously, members of different classes and families diversify their anatomies and physiologies, depending on which processes and regulation each compartment selects. The location of a conserved process (the compartment map) between diversified processes has been called the “bowtie effect” by Csete and Doyle (2002), who discuss its design benefits.
Other forms of regulatory compartmentation also facilitate diverse combinatorial uses of the gene repertoire while reducing pleiotropic interference. Each of the several hundred differentiated cell types of vertebrates is probably controlled by a few transcription factors and signaling proteins encoded by master regulatory genes, which select the expression of other regulatory genes and core processes of that cell’s phenotype. In the temporal dimension, developmental stages such as the embryo, larva, and adult are sometimes compartmentalized by expressed heterochronic genes (Abbott et al., 2005) that select stage-specific target genes, and in sexual dimorphism, target genes are selectively expressed in each sex.
To summarize, we argue that robustness, adaptability, modularity, capacity for weak regulatory linkage, exploratory behavior, and state selection of the conserved core processes, as well as the regulatory compartmentation of the conserved core processes, are key properties of the animal’s phenotype that facilitate the generation of anatomical and physiological variation by regulatory change, which ultimately requires genetic change to be heritable. These special properties reduce the number of