Pathogens past and present - reconstructing historical and ancient host jumps

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Over the past decades, the rapid development of techniques optimised to sequencethe DNA of post-mortem, museum, and archaeological specimens, termed 'ancientDNA sequencing', has provided unprecedented opportunities to recover genomes of amultitude of species at specific points in their evolutionary history. Identification of thegenomes of microbes within ancient DNA can pinpoint when a pathogen first started tocirculate in a species, inference of past transmissions and identification of genomicdeterminants of host-adaptation and infectivity. Such observations can be combinedwith contemporary clinical and veterinary infection data in an analytical frameworkthat unveils the path to host-microbe associations today. This PhD project will harnessthe unique potential of combining ancient and modern microbial genomic data toaddress major questions including: i) How has the spread of microbes betweenhumans and other animals been maintained or changed over history? ii) What is thedirection of transmission of major microbes associated to humans and animals? iii)What genomic features are enriched in pathogens infecting specific hosts and whendid they evolve? During the PhD, the student will screen published and newlygenerated data obtained from a range of historic and archaeological material toinclude key zoonoses of humans and swine (eg. Salmonella. Erysipelothrix, Yersinia)and other relevant domesticates spanning the Neolithic through to present. Using skillsinitially learned during the rotation project, analyses will be applied includingmetagenomic classification, population genetics and phylogenetic tip-dating. Usingpan-genome reconstruction methods, proteins correlated with changing hosts will beidentified as putative adaptive mechanisms including estimation of when they evolved.Results will be contextualised via collaboration with archaeologists, epidemiologists,and microbiologists. Taken together, this PhD will take advantage of the expandingtoolkit of ancient genomics to address the contemporary challenge of zoonotic diseasefrom a novel historic perspective.