Understanding the evolutionary history of the papillomaviruses

This thesis focuses on the evolutionary history of the papillomaviruses (PVs) using phylogenetic approaches. Two aspects have been examined: the first is the level of phylogenetic compatibility among PV genes and the second is determining the ancestral diversification mechanisms of the PVs in order to explain the origin of the observed associations with host species. Bayesian phylogenetic analysis has been used to make evolutionary inferences. The existence of phylogenetic compatibility among genes was examined by estimating constrained and unconstrained phylogenies for pairs of PV genes. The Bayes' factor statistic derived from comparison of the constrained and unconstrained models indicated significant evidence against identical phylogenies between any of the 6 PV genes investigated and may indicate the existence of ancestral recombination events. The formation of new host-virus associations can occur via a process of 'codivergence', where, following host speciation, the ancestral virus association is effectively inherited by the descendant host species; 'prior divergence' of the virus, which results in multiple virus associations with the host; and 'host transfer', in which the virus lineage is transferred between contemporaneous host species. To distinguish between these mechanisms of virus diversification, an approach based on temporal comparisons of host and virus divergence times was devised. Difficulties associated with the direct estimation of PV divergence times led to the incorporation of a biased sampling approach into Bayesian phylogenetic estimation. This allowed for viral divergence events to be biased in favour of codivergence but allowed sampling of times that violate this assumption and therefore indicate either prior divergence or host transfer. Statistical evaluation of the proportion of violations at each viral divergence identified significant evidence of prior divergence events behind many of the observed PV-host associations and one ancestral host transfer event