Fifteenth century CE Bolivian maize reveals genetic affinities with ancient Peruvian maize

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 Bolivian maize dating to ~500-600 BP, included as an offering with the mummified remains of a young girl. These data are compared to 16 previously published archaeological maize samples spanning at least 5000 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. During the period of interaction between the Inca state and local polities in the central Andes and consequent interactions with local agricultural traditions, the genetic diversity of maize increased. Ovule development in modern maize was selected and compared to those in archaeological specimens, revealing evidence of targeted breeding strategies aimed at improving seed quality and yield. While the cultural origin of the maize - either Inca or local Aymara - is uncertain, we demonstrate that the samples are most similar to Peruvian maize and potential targeted selection strategies for enhanced growth were well established by the 15^th century.