Implementing Single-Stranded DNA Library Preparation for Accessing The Population History of Pre-Colonial Maritime Societies of São Paulo State

• Grant number: 25/04976-0
• Support Opportunities: Scholarships abroad - Research Internship - Master's degree
• Start date: August 20, 2025
• End date: February 19, 2026
• Field of knowledge: Humanities - Archeology - Prehistoric Archaeology
• Principal Investigator: André Menezes Strauss
• Grantee: Carolina Eva Padilha
• Supervisor: Kathrin Naegele
• Host Institution: Museu de Arqueologia e Etnologia (MAE). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Institution abroad: Max-Planck-Institut Für Evolutionäre Anthropologie, Germany
• Associated to the scholarship: 23/16983-5 - Population history of pre-colonial maritime societies of São Paulo State (Brazil): an archaeogenetic analysis of the Piaçaguera shellmound, BP.MS

Abstract

Sambaquis are mounds formed by the long-term, intentional accumulation of seashells and marine fauna remains, found intermittently along the Brazilian coasts and rivers. These constructions mark human presence in coastal regions during the Holocene, between 8,000 and 1,000 years before present (kaBP). The population history of sambaqui-building groups has been extensively studied using cultural and bio-anthropological markers, and more recently, through ancient DNA (aDNA) analyses. As part of the ongoing master's project associated with this international internship proposal, bone samples from 20 individuals from the Piaçaguera coastal shell mound in São Paulo were processed at the Archaeogenetics Laboratory of the Museum of Archaeology and Ethnology (for sampling and DNA extraction) and at the Max Planck Institute for Evolutionary Anthropology (for sampling, DNA extraction, indexing, and sequencing). Preliminary results based on nuclear and mitochondrial data suggest that the Piaçaguera group is more closely related to nearby riverine shell mound populations than to more distant coastal groups. However, aDNA sequencing in the region remains limited due to poor DNA preservation, a common challenge in tropical environments. To improve the resolution of genomic data from these contexts, the main objective of this proposal is to implement new library preparation techniques designed to increase efficiency when working with highly degraded DNA. Specifically, the single-stranded DNA library preparation protocol will be applied. As this advanced method is not yet available at the University of São Paulo, the internship at the Max Planck Institute represents a unique opportunity for a Brazilian student to acquire and transfer this expertise to the home institution.