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

Abstract

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 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. 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 15th century. Significance StatementMaize has been improved through selective breeding delivering desirable horticultural, agronomic, and cultural characteristics, related to environment, nutrition, etc. Inca culture was closely associated with maize diversity, but there is little evidence to show how and why culture influenced that diversity and modern maize biogeographic patterns in South America. We show that in the 15th century CE, maize diversity in the central Andes was enhanced through selection for specific traits associated with reproduction. We hypothesize that this may have contributed to maize becoming a staple under the Inca, as happened previously with expanding Tiwanaku interactions and influence during the Middle Horizon.