Scourge of the Empire? Ancient Pathogen Genomics and the Biosocial Context of Malaria in Imperial Period Southern Italy (1st-4th c. A.D.)

Abstract

The complementarity of ancient DNA lends itself to integration with paleopathological inquiries of disease, particularly in scenarios where there is limited or conflicting historical, skeletal, and archaeological information in a given spatio-temporal context. This thesis expands on molecular approaches applied to the detection of “invisible” pathogens associated with non-catastrophic morbidity and mortality that are embedded in a unique biosocial context of the disease experience. Presented in ‘sandwich-thesis’ format, I explore the historical narrative surrounding malaria in Imperial period Italy (1st-4th c. A.D.) using a molecular approach that is integrated with an ecosocial framework, as well as addressing the methodological challenges of identifying pathogens in contexts without a priori knowledge or incongruous evidentiary sources. My research presents the first partial mitochondrial genome for P. falciparum recovered from two adults (prioritized from a subset of 58 individuals) in disparate ecological and social localities in Imperial period Italy. This provides a timestamp for this ancient protozoan parasite, with an emphasis on a multi-faceted approach to frame the human-parasite-vector-environment interactions in the studied localities. Additionally, I successfully applied an in-solution hybridization capture technique designed to detect over 1,000 human pathogens in archaeological samples, both of known and unknown pathogen constituents. This technique qualitatively and quantitatively assesses the likelihood of low abundance pathogenic targets that are present, in order to prioritize candidates to further pursue with downstream analyses, as well as beginning to explore the synergistic landscape of pathogen-pathogen interactions. In combination, the research outlined in this thesis emphasizes the molecular and biosocial experience of disease as interconnected elements in dynamic epidemiological environments of the past.