Pathogens past and present - reconstructing historical and ancient host jumps

Over the past decades, the rapid development of techniques optimised to sequence
the DNA of post-mortem, museum, and archaeological specimens, termed 'ancient
DNA sequencing', has provided unprecedented opportunities to recover genomes of a
multitude of species at specific points in their evolutionary history. Identification of the
genomes of microbes within ancient DNA can pinpoint when a pathogen first started to
circulate in a species, inference of past transmissions and identification of genomic
determinants of host-adaptation and infectivity. Such observations can be combined
with contemporary clinical and veterinary infection data in an analytical framework
that unveils the path to host-microbe associations today. This PhD project will harness
the unique potential of combining ancient and modern microbial genomic data to
address major questions including: i) How has the spread of microbes between
humans and other animals been maintained or changed over history? ii) What is the
direction of transmission of major microbes associated to humans and animals? iii)
What genomic features are enriched in pathogens infecting specific hosts and when
did they evolve? During the PhD, the student will screen published and newly
generated data obtained from a range of historic and archaeological material to
include key zoonoses of humans and swine (eg. Salmonella. Erysipelothrix, Yersinia)
and other relevant domesticates spanning the Neolithic through to present. Using skills
initially learned during the rotation project, analyses will be applied including
metagenomic classification, population genetics and phylogenetic tip-dating. Using
pan-genome reconstruction methods, proteins correlated with changing hosts will be
identified 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 expanding
toolkit of ancient genomics to address the contemporary challenge of zoonotic disease
from a novel historic perspective.