Madzima, T. | bioRxiv Science

bioRxiv2025

A comparison of tools and read depth criteria for genuine single nucleotide polymorphism identification in ancient maize samples

Maize is an important subject in the study of ancient DNA (aDNA) due to its profound historical, cultural and economic significance. Studies of maize aDNA can provide insights into domestication, evolution and gene flow of this important crop plant. During analysis of aDNA samples, it is essential to elucidate the extent of post-mortem damage (PMD) as well as to select optimal tools and read depth criteria for genuine single nucleotide polymorphism (SNP) discovery. To date, standardized approaches to address these issues are lacking. Using eight archaeological maize samples from publicly available datasets, we compared the performance of two different approaches for solving PMD, Rm5nt and NoChange. We also compared three different analysis tools (GATK, angsd and pileupCaller) and read depth criteria (2X, 5X and 10X) for genuine SNP discovery of aDNA maize samples. The results showed that the Rm5nt approach performed better in processing aDNA. We also found that the angsd tool with a read depth >= 5X is optimal for inferring the closest relative of the aDNA maize samples used in this study. Our study aims to improve the current standardized approach, including optimal approaches, tools and read depth criteria, to improve the accuracy of aDNA data interpretation. Furthermore, our results offer a practical guideline for researchers seeking to improve the quality of their aDNA data for downstream analysis.

genomics↗

bioRxiv2025

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

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.

plant biology↗