Archaeological Bolivian maize genomes suggest Inca cultural expansion augmented maize diversity in South America

Previous archaeological and anthropological studies have demonstrated the myriad of ways that cultural and political systems shape access to food and food preferences. However, few studies have conducted a biocultural analysis linking specific genotypic/phenotypic traits as evidence of cultural selection in ancient contexts. Here, we provide insight into this topic through ancient genome data from Bolivia dating to ~500 BP, included as an offering with the mummified remains of a young girl, including 16 archaeological maize samples spanning at least 5,000 years of evolution, and 226 modern maize samples. Our phylogenetic analysis showed that the archaeological Bolivian maize (aBM) has the closest genetic distance to the archaeological maize from ancient Peru, which in turn shared the most similarities with archaeological Peruvian maize. With the increased presence of the Inca state in the central Andes and its interactions with local agricultural traditions, genetic diversity of maize increased. The ovule development process was selected from modern maize and was compared to archaeological maize; where it indicates the breeding programs aimed at enhancing seed quality and yield in modern maize. Our study provides insights into the complex biocultural role that Inca Empire expansion, including its economic, symbolic and religious cultural practices, may have had in driving the expansion of maize diversity in South America.