19A major outstanding question in human prehistory is the fate of hunting and gathering populations 20 following the rise of agriculture and pastoralism. Genomic analysis of ancient and contemporary 21Europeans suggests that autochthonous groups were either absorbed into or replaced by expanding 22 farmer populations. Many of the hunter-gatherer populations persisting today live in Africa, perhaps 23 because agropastoral transitions occurred later on the continent. Here, we present the first genomic 24 data from the Chabu, a relatively isolated and marginalized hunting-and-gathering group from the 25 Southwestern Ethiopian highlands. The Chabu are a distinct genetic population that carry the highest 26 levels of Southwestern Ethiopian ancestry of any extant population studied thus far. This ancestry has 27 been in situ for at least 4,500 years. We show that the Chabu are undergoing a severe population 28 bottleneck which began around 40 generations ago. We also study other Eastern African populations 29 and demonstrate divergent patterns of historical population size change over the past 60 generations 30 between even closely related groups. We argue that these patterns demonstrate that, unlike in Europe, 31Africans hunter-gatherers responded to agropastoralism with diverse strategies. 32
33Since the beginning of the Holocene 12,000 years ago (ya), the dominant mode of human subsistence 34 has shifted from hunting and gathering to agriculture through a process known as the Neolithic 35 transition. Whether this transition occurred primarily through the mass movement of people from 36 centers of domestication (demic diffusion) or through the cultural transmission of agricultural practices 37 (cultural adoption) is still debated in archaeology, genetics and anthropology (1, 2). As this transition 38 largely concluded by 4,000 ya in Europe and Asia, there remains little direct evidence of on-the-ground 39 interaction between hunter-gatherers and agriculturalist migrants. Theoretically, in the face of 40 displacement and conflict over resources, hunter-gatherer populations might respond in a variety of 41 ways: 1) intermarry with the migrant group and adopt their agropastoral subsistence practices 42 (substantial genetic exchange); 2) adopt the subsistence practices of the migrants without intermarriage 43 (limited genetic exchange); 3) reduce their geographic range or resource acquisition (leading to a decline 44 in population size); 4) enter into an economic-symbolic exchange relationship with the migrant group; or 45 5) move to an ecological region that is marginal for pastoralism or agriculture (3, 4). These are not 46 mutually exclusive; the history of any particular hunter-gatherer group may involve multiple modes of 47