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In Chapter 3, John Gerhart and Marc Kirschner accept the notion that regulatory changes are of central importance, and indeed they argue that most key phenotypic evolution over the past 600 million years has resulted from altered usage patterns in a large set of otherwise conserved core genetic components that direct organismal development and physiology. In the “theory of facilitated variation” by Gerhart and Kirschner, several regulatory features of the genome collude to foster more phenotypic evolution with less genetic change than would otherwise have been possible.

In Chapter 4, Adam Wilkins examines the converse of evolutionary plasticity: phenotypic constraint. It has long been evident that phylogenetic legacies and developmental contingencies restrict (albeit to a debatable degree) the suite of evolutionary pathways potentially available to any species. Wilkins proposes that in addition to these conventionally recognized inhibitors of phenotypic evolution, inherent constraints also operate at the levels of interacting genes and complex genetic networks. If molecular biologists can illuminate the genetic biases that constrain as well as promote the evolution of particular phenotypes, it might become possible, Wilkins argues, to specify the relative probabilities of alternative evolutionary trajectories (at least over the short term) for particular lineages. Traditionally, this kind of predictability about evolutionary futures had been regarded as essentially impossible.

In the final chapter of Part II, Michael Lynch reminds us that mechanistic explanations of phenotypic evolution that emerge from the fields of developmental biology and molecular genetics cannot violate the fundamental dynamics of the evolutionary process as elucidated by a century of work in theoretical population genetics. Regardless of which genes underlie complex or other phenotypes, their microevolutionary dynamics remain governed by the forces of mutation, gene flow, natural selection, recombination, and random genetic drift. The point, however, is not to claim priority for one discipline over another, but rather to emphasize that any evolutionary model that disregards population genetic reality does so at its peril. To illustrate his argument, Lynch examines the ineluctable consequences of genetic drift, especially in small populations, and he highlights a wide assortment of genic and genomic phenomena that make sense only after accounting for variation among taxa in the relative power of nonadaptive evolutionary forces.

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