DOI: 10.5061/dryad.w6m905qtd
title: 15th century CE Bolivian maize reveals genetic affinities with ancient Peruvian maize

description: 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.
description: # 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 Gigante rock shelter. ancientEG85: ancient EG85 sample from El Gigante rock shelter. ancientEG90: ancient EG90 sample from El Gigante rock shelter.  ancientSM10: ancient SM10 sample from Mexico: San Marcos cave, Tehuacan Valley. ancientSM3: ancient SM3 sample from Mexico: San Marcos cave, Tehuacan Valley  ancientSM5: ancient SM10 sample from Mexico: San Marcos cave, Tehuacan Valley. ancientTehuacan162: ancient SM10 sample from Mexico: San Marcos cave, Tehuacan Valley. ancientZ2: ancien Z2 sample from Brazil:Peruacu Valley, Boquete cave.  ancientZ6: ancien Z2 sample from Brazil:Peruacu Valley, Boquete cave.  ancientZ61: ancient  Z61 sample from Peru:Ancash. ancientZ64:  ancient  Z64 sample from Peru:Ancash. ancientZ65: ancient  Z65 sample from Peru:Inca. ancientZ66: ancient Z66 sample from Argentina:Catamerca.      ancientZ67:  ancient Z67 sample from Argentina:Jujuy.     ## Code/software R and Linux; R is required to run all XXX.R scripts; the script was created using R version R version 4.4.1. Linux is required to run XXX.sh shell scripts. All scripts available on Zenodo under Software Related Work link. mapDamage-array.sh: It was used to verify cytosine deamination profiles consistent with ancient DNA, and estimated the misincorporation frequencies for all ancient maize samples. Geographic-Map.R: It was used to util latitude and longitude information, the samples were plotted on a geographic map. Geographic data visualization was carried out in R using the ggplot2, sf, leaflet, rnaturalearth, rnaturalearthdata, ggspatial, and rnaturalearthhires packages. f3.R: The admixr package, which is part of the ADMIXTURE software suite, was used to detect evidence of admixture involving aBM. PCA.R: Principal Component Analysis (PCA) was applied for all ancient and modern mazies. targetgene_within5K.R: It was used to identify target genes within a 5kb distance. xpehh_controlVScase.R: It was used to find selection between ancient and modern maize populations. ## Access information Other publicly accessible locations of the data: * Dryad Data was derived from the following sources: * All the following samples information except archaeological Bolivian maize sample 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) * All the modern samples was obtained from the following publication: [https://doi.org/10.1111/tpj.16123](https://doi.org/10.1111/tpj.16123)