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. The genetic differentiation implies that the Inca state aided maize diversity. The ovule development process was selected from modern maize and was comp..., , , # 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...,

过往考古学与人类学研究已证实，文化与政治系统可通过多元途径影响食物获取途径与饮食偏好。然而，鲜有研究开展生物文化分析，将特定基因型/表型特征作为古代背景下文化选择的实证依据。本研究依托玻利维亚距今约500年前的古代基因组数据（该样本作为陪葬品与一名年轻女孩的木乃伊遗骸一同出土）、16份涵盖至少5000年演化历程的考古玉米样本，以及226份现代玉米样本，对该议题展开深入探讨。系统发育分析结果显示，玻利维亚考古玉米（archaeological Bolivian maize, aBM）与秘鲁古代考古玉米的遗传距离最近，而秘鲁古代考古玉米又与智利沿海阿里卡地区的古代考古玉米相似度最高。遗传分化结果表明，印加帝国曾助力玉米多样性的发展。胚珠发育过程的选择源自现代玉米，并于[原文截断]。
# 考古玻利维亚玉米基因组揭示印加文化扩张提升南美玉米多样性

本研究已上传最终的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据（文件名为final_full_snps.vcf）、R脚本（包括Geographic-Map.R、common-xpehh_SelectionVScontrol.R、f3.R、PCA.R以及targetgene_within5K.R）与Shell脚本（mapDamage-array.sh）。

## 数据与文件结构说明
1. **final_full_snps.vcf**：包含17份考古样本的单核苷酸多态性信息。
2. **ancientaBMComb**：玻利维亚考古玉米样本。
3. 下述所有样本的信息均取自已发表文献：
- [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)
4. **ancientArica4**：来自智利阿里卡沿海地区的古代Arica4样本。
5. **ancientArica5**：来自智利阿里卡沿海地区的古代Arica5样本（原文此处存在笔误，标注为ancientArica4）。
6. **ancientEG84**：来自[原文截断的El...]地区的古代EG84样本。