The importance and application of the ancestral recombination graph

One of the most important evolutionary forces is recombination, it increases genetic diversity and promotes adaptation through exchange of genetic material and where existent mutations are shuffled. Knowledge about recombination is, for example, fundamental to understand genome structure (Reich et al., 2001), phenotypic diversity (Zhang et al., 2002), and diverse genetic diseases (Daly et al., 2001). Indeed, recombination should be considered to properly study molecular evolution and perform phylogenetic inferences (e.g., Schierup and Hein, 2000; Anisimova et al., 2003; Arenas and Posada, 2010c). The recombination evolutionary history is commonly represented by the ancestral recombination graph (ARG) (Griffiths and Marjoram, 1997), an illustrative example is shown in Figure 1. Counterintuitively, ARGs have not been widely used, perhaps as a consequence of the difficulties to infer explicit ARGs and the complexity of the ARG representation. The aim of this general commentary is to describe the importance and application of the ARG.