Decoding the Past: Ancient Genomics and the Histories of the Classic Maya Civilisation

Abstract

The Maya civilisation, renowned for its advanced urban centres, sophisticated architectural achievements, and rich cultural heritage, stands as one of the most well-known and influential ancient societies. Understanding this history not only deepens our knowledge of past civilisations but also provides valuable insights into societal resilience offering lessons that can help modern human societies adapt, survive, and thrive in the face of contemporary global challenges. However, the genetic history of the ancient Maya remains relatively understudied. This thesis presents seven newly sequenced genomes from the city-state of Copan during the Classic Maya period, including a dynastic ruler and his sacrificial companion. Population structure analyses reveal genetic continuity in the Maya region from the Late Archaic period to the present, alongside an influx of highland Mexican ancestry appearing as early as the Early-to-Middle Classic period. To enhance the resolution of ancient genomic data, this thesis also evaluates GLIMPSE, an imputation tool for low-coverage ancient genomes. Imputation was assessed across two high-coverage ancient individuals. GLIMPSE consistently achieved high accuracy, particularly at homogenous sites, while heterogenous sites exhibited improved performance above 0.1�. Leveraging these methodological advancements, this thesis reconstructs demographic patterns across ancient American populations using imputed genomes. Analyses of identical-by-descent (IBD) segments and runs-of-homozygosity (ROH) confirm small founding population size in most hunter-gatherers, but not populations from the Early Holocene. In the Maya people, demographic reconstruction reveals substantial growth coinciding with the incorporation of fully domesticated maize. These demographic insights also contribute to the broader understanding of civilisation decline and societal transformations: population size estimates in the Maya region directly depict a decline coinciding with the Maya collapse.