Emerging infectious diseases (diseases that have newly appeared in a population1; EIDs) are one of the greatest threats to human health and global stability 2–4. However, for almost all EIDs, nothing is known of their prevalence in the past. This historic information is essential for assessing trajectories of population abundance, and in turn determine whether a disease is genuinely newly emerging, and any long-term changes in prevalence5. An understanding of the presence/absence of parasites in the past would enable contextualisation of present-day parasite diversity, providing a springboard for future studies to confirm or update EID priorities and classifications. Wildlife archives (bone pathology and macroparasites) at Aberystwyth University (School of Veterinary Science) will be used as references to identify pathological specimens in zooarchaeological and museum assemblages. Bioinformatic methods (e.g. 6) will be used to molecularly identify the presence of parasites in publicly available whole genome sequencing data, and newly generated shotgun sequencing data, and from the reference and ancient faunal remains. Overlap will be assessed between the reference and ancient datasets, and the morphological and molecular approaches will be compared to assess Type I and Type II error. We will use contextual information and 14C dating to identify the first occurrence of any parasite DNA identified. The project will focus on large- and medium-bodied mammals from archaeological archives and museum collections (including Cardiff Archaeology and the NHM, London), dating from the Holocene (c. 11.7 KYA) until the present-day. Ancient molecular labwork will be carried out at the newly formed Cardiff University ancient DNA (CUAD) laboratory.
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