**1. Introduction**

36 Gene Duplication

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Gene duplication has long been recognized as a powerful mechanism facilitating development and evolution in genomes. Duplication events produce additional copies of genomic information, perhaps including one or more genes. While in some cases these duplicated elements may be of immediate benefit (i.e. increasing availability and effective dosage of a desired gene product), often they are initially at least somewhat redundant, and either neutral or mildly detrimental to the fitness of the organism. It is perhaps no surprise, then, that the majority of duplicated genes are quickly deactivated by mutations abolishing transcription or translation. Some duplicated genes, however, survive and persist, suggesting that their retention has some benefit. Many of these genes seem to have acquired properties that distinguish them from their progenitors – they may be expressed in a novel tissue type, for example, or differ in their functional specificity. In these cases, it appears as though duplication has facilitated evolution, either by allowing specialization and refinement or, perhaps most intriguingly, generating genes free to mutate and acquire 'novel' functions. These retained duplicates form a family of genes related through common ancestry. As a result of their common origin, gene sequences within gene families are often quite similar, complicating the task of assigning them unique and specific functions. As such, there has been a significant effort to study and characterize the evolution of function in the aftermath of a duplication event. This chapter will briefly cover the various modes of gene duplication, and then will focus on the various functional outcomes of duplication. The theoretical models for functional specialization following a duplication event are discussed, as are practical techniques for applying these models to observed gene duplicates.
