The evolution of gene duplicates.
Gene and genome duplications have given rise to enormous variability among species in the number of genes within their genomes. Gene copies have in turn played important roles in adaptation, having been implicated in the evolution of the immune response, insecticide resistance, efficient protein synthesis, and vertebrate body plans. In this chapter, we discuss the life history of gene duplications, from their first appearance within a population, through the period during which they rise in frequency or disappear, to their long-term fate. At each phase, we discuss the evolutionary processes that have influenced the dynamics of gene duplications and shaped their ultimate roles within a population. We argue that there is no evidence that organisms have evolved strategies to promote gene duplication in order to permit adaptive evolution. In contrast, many mechanisms exist to silence or eliminate duplicated genes, suggesting that selection has acted largely to reduce the rate of gene duplication. We also argue that natural selection has functioned as an effective sieve, increasing the representation of beneficial gene duplicates among those that establish within a population and that play a long-term role in evolution. To refine our understanding of how selection acts on new gene duplications, we provide a model incorporating a single-copy gene, its gene duplicate, and selection either favoring heterozygotes or eliminating deleterious mutations. Although both forms of selection can increase the initial rate of spread of a gene duplicate, the efficacy with which they do so differs dramatically. Heterozygote advantage always increases the rate of spread and can have a large impact. In contrast, masking deleterious mutations never has a large effect on the rate of spread of the duplicate, and this minor effect can be negative as well as positive. In both cases, the degree of linkage between the two gene copies affects the rate of spread of the duplication. Finally, we discuss evolutionary processes that occur over longer periods after a gene duplication has become established within a population. These long-term processes include maintenance, inactivation, and diversification in function. Consideration of each of the short-term and long-term processes affecting duplicated genes illustrates the subtle ways in which selection has acted to shape genomic structure.