occur throughout the genome, although perhaps not at uniform frequency, and include changes of single bases or short sequences or even long segments of DNA (Feuk et al., 2006). Some genetic changes are lethal, some are neutral, and fewer are viable and selectable. Furthermore, the understanding of variation has advanced with the knowledge that DNA sequences encode RNA and protein, because the latter two would bear the marks of DNA sequence change and, in principle, alter the phenotype. Also, discoveries of gene regulation have opened the possibility of important evolutionary changes in nontranscribed DNA sequences, as well. Still, there are no “laws of variation” regarding its generation, only a black box of chaotic accidents entered by genetic variation and occasionally exited by selectable phenotypic variation.
In the past 20 years, enormous insights have been gained about the development and physiology of animals, namely, about the generation of their phenotype from their genotype, the kind of information eventually needed to explain and predict phenotypic change from genetic change. From these advances, can something now be said about the nature of phenotypic variation and its dependence on genetic change? What is really modified in descent with modification? Have all components of a new trait been modified a little, or a few elements a lot while others not at all? Are many genetic changes needed for a modification of phenotype or only a few? Are there preferred targets for change? Are there cryptic sources of variation? These questions require concrete answers that can come only from in-depth studies of the phenotype, that is, the animal’s development and physiology.
We propose that the phenotype of the organism plays a large role in (i) providing functional components for phenotypic variation and (ii) facilitating the generation of phenotypic variation from genetic change. We outline a set of concepts from others and ourselves, organized in a theory of facilitated variation, to connect genetic and phenotypic variation (see Kirschner and Gerhart, 2005, for a longer presentation). Like other theories (King and Wilson, 1975; Carroll et al., 1995; Davidson, 2006), it identifies regulatory changes as ones particularly important for animal evolution, but unlike others it also emphasizes the targets of regulation.
We include four steps from genetic variation to viable phenotypic variation of anatomy and physiology, and we wish to show at which steps the facilitation of variation occurs, and how it occurs. First, as widely accepted, genetic variation arises from recent mutations and rearrangements of the genome and from standing genetic differences arranged in new combinations by sexual reproduction. Second, particular genetic variations then lead to regulatory changes, namely (i) changes of DNA sequences at cis-regulatory sites; (ii) changes of DNA at sites transcribed into RNA regulatory regions, such as those for RNA stability, trans-