The social system of geladas (Theropithecus gelada) and hamadryas baboons (Papio hamadryas hamadryas), characterized by a multilevel structure based upon one-male reproductive units, is unique among primates. Population genetic theory predicts that the semiclosed, substructured social groupings exhibited by these taxa should result in increased relatedness among group members, possibly facilitating relatively rapid rates of evolution when compared to taxa without similarly subdivided populations. In this chapter, we test these predictions by quantifying a mobile genetic element known as baboon endogenous virus (BaEV). Quantitative real-time PCR methods were used to assess relative BaEV copy numbers in captive and wild-caught baboons, including samples from geladas, Guinea (P. h. papio), olive (P. h. anubis), and hamadryas baboons, as well as in individuals with varying degrees of olive and hamadryas ancestry. Results show that geladas possess significantly higher BaEV copy numbers when compared to Papio baboons, and that African hamadryas show a trend toward higher BaEV copy numbers within Papio baboons. These findings illustrate the impact of social organization and reproductive systems on genome evolution, suggesting that hierarchically organized gelada and hamadryas societies (i) promote relatively greater degrees of inbreeding than in their close papionin relatives and (ii) provide conditions under which maintaining an increased BaEV element number confers a selective advantage.