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Summary There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today’s genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000–500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. Video Abstract

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Recent arguments stating that marine resources were relatively unimportant in cultural developments on the coast of Peru during the Preceramic Period are incorrect on several counts. It is shown that the economics and technology of maritime subsistence of coastal Peru are more complex than previously thought, that the nutritional values of terrestrial versus maritime foods are debatable, that the dynamics of El Niño events are complex, and that maritime resources must still be seen as important for Preceramic Period economies. [Central Andes, coastal adaptations, ecological anthropology, origins of complex societies]