15th 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 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 i..., , , # Archaeological Bolivian maize genomes suggest Inca cultural expansion augmented maize diversity in South America

We have submitted our final SNP data (final_full_snps.vcf), R script (Geographic-Map.R, common-xpehh_SelectionVScontrol.R , f3.R, PCA.R, and targetgene_within5K.R), and Shell script (mapDamage-array.sh).

## Description of the data and file structure

\"final_full_snps.vcf\": contains the snps informations for 17 archaeological samples.

ancientaBMComb: archaeological Bolivian maize sample.

All the following samples information was obtained from previous publications:

[DOI:10.1126/science.aav0207](https://doi.org/10.1126/science.aav0207)

[https://doi.org/10.1073/pnas.2015560117](https://doi.org/10.1073/pnas.2015560117)

[https://doi.org/10.1073/pnas.1609701113](https://doi.org/10.1073/pnas.1609701113)

ancientArica4: ancient Arica4 sample from Arica, Chile, coastal.

ancientArica5: ancient Arica4 sample from Arica, Chile, coastal.

ancientEG84: ancient EG84 sample from El...,