Infectious diseases have had an intimate history with humans and have shaped our genetic makeup through generating strong selective pressures. Although disease emergence and epidemics occur on a local scale, human interrelationships formed through travel and trade can lead to exchanges of pathogenic communities. While such transfers were common among the interconnected Eurasian and North African cultures throughout most of human history, the rest of the world experienced relative ecological autonomy. The terminal Pleistocene witnessed the colonisation of vast territory on the American continents, after which interactions between New and Old World peoples were limited for millennia by geographical barriers. These ecological worlds collided at the end of the fifteenth century, when improvements in navigation and the discovery of the Americas by Europeans permitted regular contact and plentiful opportunities for biological interchange. The identities of most diseases that played leading roles during this period of exchange are known, though details on the directions of their movement and temporal introductions remain the subject of scholarly debate. The work programme presented here will use an underexplored data source – ancient pathogen genomes – to identify infectious insults in pre- and post-contact New and Old World skeletal series, thus enabling an evaluation of changing disease landscapes at contact. Complementary to this goal, genomic loci for human immunity genes will be interrogated, thus permitting quantitative evaluations of disease adaptation. Ancient molecular data will be acquired through use of the most sensitive and up to date methods in the field of ancient DNA with the aim of bringing diseases not easily seen from skeletal morphology or historical documents to light in clear detail. This will permit an unprecedented resolution of past disease experience and host-pathogen interactions during this dynamic period of global ecological unification.
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