Ancient DNA from pre-Columbian South America

Abstract

Ancient DNA (aDNA) research in the Americas represents a genetic strategy to investigate demographic and historical events of populations in the continent with the added bonus of having a direct and temporal perspective. This thesis aims to explore human mitochondrial DNA (mtDNA) diversity from a large number of pre-Columbian samples in a diachronic transect through time in order to refine our understanding of the genetic structure and diversity of ancient civilizations in the Central Andes of South America prior to the arrival of Europeans. I used a combination of traditional PCR-based methods and the latest technological advances for DNA analysis (i.e. Next-Generation Sequencing – NGS) to generate high-resolution mtDNA data to explore the past genetic diversity of South American populations. This work shows the perspective of aDNA research to identify temporal transitions in the genetic composition in the Central Andes of South America in real-time, since I aimed to incorporate samples from all cultural archaeological periods, improving the spatial and geographic coverage. By comparing the results with genetic data from modern-day native populations, this thesis will also address the potential impact of the European colonization on indigenous populations to understand the evolutionary history of Native Americans. To that end, the acquisition of high-resolution genomic data from ancient specimens showcase the true potential of aDNA research to uncover (re-discover) lost genetic diversity or lost mtDNA lineages from pre-Columbian populations, which cannot be inferred from modern-day populations. I aim to provide an accurate description of patterns of genetic diversity through time, reconciling and contrasting the genetic data with valuable archaeological information, and to test for demographic and population continuity or discontinuity in pre-contact South America. Finally, this thesis adds important perspective to the existing knowledge about mtDNA diversity and population prehistory in the Central Andes.