At the end of gastrulation, the typical mammalian embryo has a pear‐shaped outline and is composed of an outer ectodermal layer, a middle mesodermal layer and an inner endodermal layer. A longitudinal column of mesoderm, the notochord, which arose from the primitive node, establishes the cranial–caudal axis of the developing embryo (Fig 9.1).

The body plan of mammalian species is directed by a genomic regulatory programme. A major influence on evolutionary change with respect to body plan has arisen through the alteration of cis‐regulatory modules that control gene expression. Cis‐regulatory modules are non‐coding DNA sequences in or near a gene which often contain binding sites for transcription factors and direct the spatio‐temporal expression of that particular gene. Complex gene regulatory networks (GRNs) which have evolved through modularisation, duplication and specialisation of simple regulatory motifs have enabled both subtle and large morphological changes to take place throughout evolution.

In the course of evolution, the trajectory of body plan development has followed what is termed the ‘hourglass model’, whereby embryos from different species are at their most morphologically divergent state during the earliest and latest stages of development. The greatest degree of conservation with respect to morphology is observed during what is termed the phylotypic period. During this time, which, in vertebrates, corresponds to the period when the undifferentiated organ primordia begin to emerge, embryos from different species bear the greatest resemblance to each other. As this highly conserved period of embryogenesis proceeds, multiple gene regulatory networks are highly interconnected within organ modules.

The characteristics of encapsulation, inheritance and polymorphism which are inherent in the object‐oriented programming paradigm used in modern day software engineering resonate strongly with the underlying logic and organisation of the regulatory networks which control many of the highly conserved mechanisms of embryonic development. In addition, the multiple inputs to a given cis‐regulatory module such as ‘and’, ‘or’, or ‘not’, or combinations of these, have enabled computational biologists to model and then predict developmental states in simple organisms according to Boolean logic. Currently a number of research groups are employing computer simulations to study the evolution of GRNs to elucidate general principles of developmental processes in embryology.

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