Among the ancient individuals analyzed here, only a ∼600 BP individual from the Zanzibar archipelago has a genetic profile similar to present-day Bantu speakers (Figure 1). Notably, this individual has even more western-African-related ancestry than the present-day Bantu speakers we analyzed from Kenya, who also derive some of their ancestry from lineages related to Dinka and Tanzania_Luxmanda_3100BP (Figure 1B). Using linkage disequilibrium, we estimate that this admixture between western- and eastern-African-related lineages occurred an average of 800–400 years ago (STAR Methods). This suggests a scenario of genetic isolation between early farmers and previously established foragers during the initial phase of the Bantu expansion into eastern Africa (Crowther et al., 2017, Ribot et al., 2010), a barrier that broke down over time as mixture occurred. This parallels the patterns previously observed in genomic analyses of the Neolithic expansion into Europe (Haak et al., 2015, Skoglund et al., 2012) and the East Asian farming expansion into Remote Oceania (Skoglund et al., 2016). However, this process of delayed admixture did not always apply in Africa, as is evident in the absence of admixture from previously established hunter-gatherers in present-day Malawians.