Genomic insights into ancestry and infectious disease in 17th-century colonial Brazil

Abstract

During urban redevelopment in the historic district of a Brazilian metropolis, archaeologists uncovered a previously undocumented 17th-century cemetery, containing the closely spaced remains of over two dozen young adult males of military age. Historical records suggest the site once housed a makeshift hospital, raising questions about the origins and causes of death of those interred, particularly given the absence of skeletal evidence for violent or fatal trauma. The current study integrates bioarchaeological, historical, and genomic data to investigate the ancestry and putative disease-related mortality of nine individuals whose remains were recovered and subsequently sequenced. Population-genetic analyses revealed strong affinities with Northern European populations, particularly from Norway, Iceland, Estonia, and Czechoslovia, consistent with their likely roles as soldiers or laborers employed by the Dutch West India Company. To explore potential causes of death, we conducted a metagenomic screening with a novel pipeline optimized for degraded DNA, which revealed widespread presence of Klebsiella pneumoniae and Mycobacterium tuberculosis pathogens across all samples. Authenticity was confirmed through post-mortem damage patterns characteristic of historical samples. These findings, together with the absence of combat trauma and the collective burial context at the site, support the hypothesis of an epidemic-related mortality event. This study contributes to the growing field of historical pathogen genomics and offers a rare genomic perspective on life, mobility, and health during a period of colonial upheaval in South America.