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Abstract
The long-term evolutionary history of many viral lineages is poorly understood. Novel sources of ancient DNA combined with phylogenetic analyses can provide insight into the time scale of virus evolution. Here we report viral sequences from ancient North American packrat middens. We screened samples up to 27,000-years old and found evidence of papillomavirus (PV) infection in Neotoma cinerea (Bushy-tailed packrat). Phylogenetic analysis placed the PV sequences in a clade with other previously published PV sequences isolated from rodents. Concordance between the host and virus tree topologies along with a correlation in branch lengths suggests a shared evolutionary history between rodents and PVs. Based on host divergence times, PVs have likely been circulating in rodents for at least 17 million years. These results have implications for our understanding of PV evolution and for further research with ancient DNA from Neotoma middens.
Highlights
A major question in viral evolution is the timescale of coevolution between host and virus (Holmes 2009)
We sought to test whether PV sequences could be recovered from ancient rodent samples, which would provide direct evidence of long-term infection
We describe ancient PV sequences derived from rodent middens, and compare them to other published rodent PVs
Summary
A major question in viral evolution is the timescale of coevolution between host and virus (Holmes 2009). If there is frequent cross-species transmission of viruses across hosts, the phylogenies will not be congruent. The evolutionary history of PVs is complex, with descriptions in the literature of both strict hostvirus codivergence in some taxa and cross-species transmission in others (Ong et al 1993; Bernard 1994; Gottschling et al 2007, 2011; Rector et al 2007; Shah et al 2010). PVs isolated from birds and turtles form a monophyletic group distinct to those from mammals, but within the mammalian PVs there is no strict pattern of codivergence that would unambiguously indicate an ancient relationship between host and virus. In the well-studied organism, humans, over 150 distinct PVs have been discovered (de Villiers et al 2004). One hypothesis for this pattern is that PVs colonized
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