The presence of many similar developmental regulatory genes among long-diverged and vastly different animals such as the mouse and the fruit fly raises an apparent paradox. If bilaterians share a related set of developmental genes, how has morphological diversity evolved? There must be genetic differences between animal lineages that direct the development of different animal morphologies. One potential source of genetic differences among animals is the coding content of their genomes, including the number and biochemical functions of toolkit genes. Another possible source is the way that toolkit genes are used during development, including both the timing and pattern of their expression and their interactions with other developmental genes in regulatory circuits and networks.
This chapter focuses on the assembly and expansion of the genetic toolkit for development during animal evolution and the role of gene evolution in the origins of morphological complexity. The number of genes contained within an evolving genome is dynamic, and gene duplication increases the information content and potential complexity of developmental programs. Representatives of large gene families are shared among bilaterians, and these families continue to evolve new members in different animal lineages. The expansion of gene families during animal evolution can be traced by comparing the genes found in extant (living) organisms and by mapping gene duplication events relative to animal phylogeny. In particular, organisms that are basal (most deeply branching) members of a clade indicate the state of the toolkit before the evolution and radiation of more recent groups.
Analysis of gene families reveals two periods of major genomic change during animal evolution that correlate with the emergence of more complex animal forms. One interval occurred at the transition to triploblastic bilaterians early in the animal tree; the other is found at the base of the vertebrate lineage. By contrast, the content of the genetic toolkit for development appears roughly equivalent among other morphologically disparate bilaterian phyla.
Species and groups of species which are called aberrant, and which may fancifully be called living fossils, will aid us in forming a picture of the ancient forms of life. Embryology will often reveal to us the structure, in some degree obscured, of the prototypes of each great class.
—Charles Darwin, The Origin of Species (1859)
Thus expansion of the toolkit correlates with increased animal complexity, but not with diversity.
Evolutionary changes in the proteins that make up the toolkit are more often not the primary source of genetic differences that underlie the morphological diversity of animal forms. Indeed, some homologous genes from long-diverged animal phyla share similar biochemical functions. More significantly, some toolkit genes have similar developmental functions, and these similarities may be used to make inferences about the possible anatomy of animal ancestors, even without fossil evidence. The shared developmental functions among disparate animal phyla suggest that these toolkit genes controled the development of various anatomical features in the last common ancestor of bilaterians.
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