Viruses are ubiquitous, obligate intracellular parasites that have had a pervasive influence on the evolutionary history of life. Despite being extensively studied due to their role in disease, very little is known about their long-term evolution, since they do not form a geological fossil record. The new field of paleovirology is the study of ancient viruses, which in the genomic age has been facilitated by discoveries of endogenous viral elements (EVEs). EVEs are the remnants of viruses that have heritably integrated into the genomes of their hosts and we were the first to discover that viruses of all genome types can endogenise. This genomic fossil record contains information about viral/host interactions that would be impossible to recover from contemporary viral sequences. We will develop novel methodologies to exploit this data source in order to quantify how viral transmission dynamics vary between organisms and over time, and to identify the factors that determine this. While most EVEs are non-functional relics, they are sometimes captured and repurposed by their hosts to serve a beneficial function as antiviral genes. These remarkable examples indicate an important role for virus to host gene flow in evolution, and we will determine the nature and extent of this phenomenon. This gene exchange is mirrored in viruses that capture host genes to evade immune responses. We will integrate bioinformatics, evolutionary, and experimental techniques, to elucidate the evolutionary processes underlying virus-host gene flow in both directions, and to determine the molecular features that impact host immunity and viral pathogenicity. Now is the time to pursue this research, given the unprecedented availability of genomic data and the emergence of paleovirology. Our results will greatly improve our understanding of viral cross-species transmission, as well as the role of gene flow on the evolutionary arms race between viruses and their hosts over geological timescales.
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