Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

Geoghegan, Jemma L.; Duchêne, Sebastián; Holmes, Edward C.

The virus families that passed these selection criteria were the Adenoviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Flaviviridae, Hepadnaviridae, Herpesviridae, Orthomyxoviridae, Papillomaviridae, Paramyxoviridae, Parvoviridae, Picornaviridae, Polyomaviridae, Potyviridae, Poxviridae, Reoviridae, Retroviridae, Rhabdoviridae and Togaviridae. Each data set contained between 23-142 viruses from a diverse range of eukaryotic hosts, including mammals, birds, reptiles, amphibians, fish, invertebrates, and plants. For the purposes of this study we regarded a virus isolated from a particular host species as a distinct virus sample worthy of analysis: for example, rabies virus isolated from a human host was deemed distinct from rabies virus isolated from a canine host. The resulting virus and host data sets included in this study comprised a diverse sample of the available data (see S2 Table for a summary of the virus and host diversity). Most data sets contained more viruses than those from their corresponding hosts because they included multiple viruses from a family that can infect the same host.