AbstractPapillomaviruses (PVs) have a wide host range, infecting mammals, birds, turtles, and snakes. The recent discovery of PVs in different fish species allows for a more complete reconstruction of the evolutionary history of the viral family. In this study we perform phylogenetic dating to analyse evolutionary events that occurred during PV evolution, as well as to estimate speciation and evolutionary rates.We have used four different data sets to explore and correct for potential biases that particular taxa combinations may introduce during molecular time inference. When considering the evolution of substitution rates we observed that short-term rate estimates are much higher than long-term rate estimates, also known as the time-dependent rate phenomenon. We discuss that for PVs the time-dependent evolutionary rates may reflect changes in the available host niches. When considering the evolution of viral branching events (as a proxy for speciation rates), we show that these are not constant through time, suggesting the occurrence of distinct evolutionary events such as adaptive radiations. In a joint analysis with host speciation rates, we identify at least four different evolutionary periods, demonstrating that the evolution of PVs is multiphasic, and refining the previously suggested biphasic evolutionary scenario.Thanks to the discovery of novel PVs in basal hosts and to the implementation of a time-dependent rate model for molecular dating, our results provide new insights into the evolutionary history of PVs. In this updated evolutionary scenario, ecological opportunity appears as one main driving force for the different radiation and key-innovation events we observe.
Pleistocene evolutionary history of the Clouded Apollo (Parnassius mnemosyne): genetic signatures of climate cycles and a ‘time-dependent’ mitochondrial substitution rate
