Time-calibrated tree reconciliations reveal frequent losses, intrahost speciations, and host switches in the evolution of herpesviruses

Cospeciation has been suggested to be the main force driving the evolution of herpesviruses, with viral species co-diverging with their hosts along more than 400 million years of evolutionay history. Recent studies, however, have been challenging this assumption, showing that other co-phylogenetic events, such as intrahost speciations and host switches play a central role on their evolution. Most of these studies, however, were performed with undated phylogenies, which may mis-estimate the frequency of certain events. In this study we performed co-phylogenetic analyses using time-calibrated trees of herpesviruses and hosts. This approach allowed us to (i) perform better estimations of co-phylogenetic events over time, and (ii) integrate crucial information about continental drift and historical biogeography to better understand virus-host evolution. We observed that cospeciations were in fact relatively rare events, which took place mostly after the Late Cretaceous (~100 Millions of years ago). Host switches were particularly common among alphaherpesviruses, where at least 10 transfers were detected. Among beta- and gammaherpesviruses, transfers were less frequent, with intrahost speciation followed by loss playing a more prominent role, especially from the Early Jurassic to the Early Cretaceous, when these viral lineages underwent several intrahost speciations. Our study reinforces the evidence that cospeciations are indeed uncommon events in herpesvirus evolution. More than topological incongruences, mismatches in divergence times were the main disagreements between host and viral phylogenies. In most cases, host switches could not explain such disparities, highlighting the important role of losses and intrahost speciations in the evolution of herpesviruses.