Archaeological Bolivian maize genomes suggest diversity is associated with Inca cultural expansion and environmental variation in South America

Abstract Previous archaeological and anthropological studies have demonstrated the myriad ways that cultural and political systems shape access to and preferences for food. However, few studies have carried out biocultural analysis linking specific genotypic/phenotypic traits as evidence of cultural selection in ancient contexts. Here, we address this issue by comparing genomes of maize samples from Bolivia dating to ~500 BP included as an offering with the mummified remains of a young girl to 13 archaeological maize samples spanning at least 5,000 years of evolution, and 87 modern western hemisphere maize samples. Our phylogenetic analysis showed that the archaeological Bolivian maize (aBM) has the closest genetic distance to archaeological maize from ancient Peru, which in turn was derived from central Mexican domesticated varieties. The comparative genomic analysis identified specific modifications in the aBM genome representing traits that were selected by ancient farmers, including shorter growing season, greater drought28 istant, and sweeter taste. The genome of the aBM appears to reflect gene flow from Chile coinciding with the arrival of the Inca empire in the altiplano region surrounding modern-day La Paz, as well as selection for specific traits related to growth in this marginal environment and taste preference. Our study provides insights into the complex biocultural role that Inca culture had in determining the direction of maize diversity in South America.