The assembly and expansion of the genetic toolkit in early metazoans and its expansion in early vertebrates were two intervals in which gene duplication and divergence played major roles in morphological evolution. However, the diversification of protostomes, most deuterostomes, and the vertebrates (after genome expansion) occurred around ancient and largely equivalent toolkits of major developmental genes. These observations lead us to conclude that changes in developmental gene regulation are the predominant genetic mechanisms underlying large-scale morphological evolution. Most of the examples in Chapters 5 and 6, however, have focused on differences between groups at higher taxonomic levels, where gross differences in the expression of major regulatory genes are correlated with morphological diversification and innovation. One implicit assumption of the case studies examined thus far is that large-scale diversity is a product of the same evolutionary and developmental mechanisms that operate on the scale of individual species. To test the validity of this assumption, we must change the taxonomic scale of our analysis and the nature of the characters under study. Because the source of morphological evolution is morphological variation, it is important to understand the genetic architecture and the molecular basis of morphological variation within species and of phenotypic divergence between closely related species.
In order to approach phenotypic and developmental evolution at the level of individual species, analyses of more variable and rapidly evolving traits are necessary. Characters such as coat color in mammals, pigmentation in insects, bristle numbers in flies, and skeletal armor in certain fishes have diverged frequently and rapidly. Because genetic studies are sometimes feasible between closely related species, dissection of the underlying genetic, developmental, and molecular bases of the divergence of some characters is possible at a much deeper mechanistic level than are slowly evolving traits among more divergent groups. Studies of
. . . remember that we are still at the beginning, that the complexity of the problem of Specific Differences is hardly less now than it was when Darwin first shewed that Natural History is a problem and no vain riddle
—William Bateson Materials for the Study of Variation (1984)
closely related or morphologically variable species have sought to address four general questions concerning the genetic and molecular mechanisms of morphological evolution, including:
1. How many and which specific genes underlie phenotypic divergence of a particular trait between species?
2. Are the same genes involved in intraspecific variation and interspecific divergence of a specific trait?
3. Are the same loci responsible for similar, independent phenotypic changes (convergence) in different lineages?
4. What is the molecular nature of genetic differences contributing to divergence (i.e. the relative contribution of regulatory and coding changes)?
This chapter uses case studies to examine the genetic architecture and molecular mechanisms underlying differences between related species or populations. The characters studied range from simple qualitative traits affected by single genes, to quantitative traits that may be influenced by variation at just a few to more than 20 loci. The architecture of genetic regulatory systems is a major determinant of the means through which evolutionary differences arise. In several cases, independent evolutionary changes in different lineages have occurred through evolution at the same genetic loci, providing striking molecular evidence for convergence. Both phenotypic divergence and variation are most often associated with noncoding, regulatory sequences, suggesting again that regulatory evolution in developmental genes is the predominant force in morphological evolution.
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