Doctoral Dissertation Research: Genomic Investigation of Ancient Pathogens and the Implications of Conquest

University Of California-Santa Cruz, Santa Cruz CA

Investigators

Abstract

When human groups first come into contact, diseases can be transmitted rapidly through previously unexposed populations. In the past, diseases during initial contact are believed to have led to mass mortality and likely influenced the outcome of colonization attempts. This doctoral dissertation project uses ancient DNA data to detect pathogens associated with conquest and colonization and determine how the pathogens evolved and why they were so deadly. The project outcomes can advance knowledge about the consequences of colonization as well as the evolution and ecology of diseases, many of which are still a struggle to treat and control today. The researchers emphasize substantive collaborations with descendant communities and community stakeholders. Local communities are actively involved in the project, and the research contributes to educational materials and museum exhibits in those regions. The project also fosters science communication and public outreach activities and provides laboratory training for undergraduates, including students from underrepresented groups in STEM. This ancient pathogen genomics project aims to identify which specific pathogens were causing the widespread deaths of Indigenous people during European conquest, how these diseases evolved in a new environment, and how different environments and/or cultural practices may have led to differences in disease spread or mortality outcomes. The study examines data generated from approximately 200 individuals from four strategically selected early contact-era sites of differing ecological and cultural environments. The researchers use gold-standard ancient pathogen genomics methods to sequence the DNA of these pathogens, determine their evolutionary trees, confirm their European origin, discover how and when they may have evolved into modern-day strains, and detect hybridization or diversification events. Where there is enough data, the researchers also perform functional analyses to identify variants through specific defining markers such as any gene loss or gain important for virulence or pathogenicity. In addition to standard high-throughput genomics and bioinformatics methods, this study incorporates historical accounts, disease ecology, and archaeological contexts to uncover a more comprehensive perspective of key events in human history. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.