Genetic polymorphism data represent the outcome of a unique historical process. The coalescent is a powerful modeling tool that makes it possible to incorporate this fact into a coherent statistical framework. Over the past 20 years, coalescent theory has come to play an increasingly important role in population genetics, and coalescent-based methods have become standard in many areas. However, methods based on classical population genetics theory or borrowed from related fields like systematics are still widely used; these methods typically fail to take the unique features of population genetic data into account.
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