tionally induced ones. Thus, genes are probably more often followers than leaders in evolutionary change. Species differences can originate before reproductive isolation and contribute to the process of speciation itself. Therefore, the genetics of speciation can profit from studies of changes in gene expression as well as changes in gene frequency and genetic isolation.
The evolution of reproductive isolation is a defining characteristic of speciation. Reproductive isolation contributes to the diversification of species by creating genetically independent lineages, the branches of a phylogenetic tree. Each branching point of the tree of life is a speciation event. However, reproductive isolation alone does not create a new branch, because by itself it cannot produce the phenotypic divergence represented by the angular departure of a branch from the ancestral form. In the book celebrated by this colloquium, Systematics and the Origin of Species (Mayr, 1942), Ernst Mayr called phenotypic divergence between populations “the other aspect of speciation.” Mayr wrote that speciation has two parts: “One part … is the establishment of discontinuities,” or reproductive isolation. “The other aspect is the establishment of diversity and divergence, that is the origin of new characters…” (Mayr, 1942, p. 23). The origin of species differences, not reproductive isolation, were the main focus of Darwin’s book On the Origin of Species by Means of Natural Selection (Darwin, 1858).
This second aspect of speciation, the origin of new characters, is the subject I address here. In particular, I will pursue Mayr’s suggestion that “the workings of this process,” the origin of new characters or novel phenotypic traits, “can best be studied if we analyze variation” (Mayr, 1942, p. 23). I will take a close look at the origins of variation, starting with two simple questions. (i) Where does the variation, or the variant that makes a new trait, come from? (ii) What gets this second, divergence part of speciation, the origin of species differences, started?
The evolutionary synthesis of the mid-20th century, sometimes called the “Neo-Darwinian Synthesis,” has been characterized as a synthesis of Darwinism and genetics, with genetic mutation seen as the source of new selectable variation. “The ‘genetical theory of natural selection,’ the theory that evolution proceeds by natural selection of ‘random’ mutations, … is the basis of the ‘neo-Darwinian synthesis’” (Leigh, 1987, p. 187). Consistent with this theory, natural selection, or fitness differences (differential reproductive success), is sometimes defined in terms of genotypes rather than phenotypes (e.g., Orr, 2005; see also review in West-Eberhard, 2003,