Diversity in a honey bee pathogen: first report of a third master variant of the Deformed Wing Virus quasispecies

Mordecai, Gideon J; Wilfert, Lena; Martin, Stephen J; Jones, Ian M; Schroeder, Declan C

To estimate the evolutionary rate of DWV and its subtypes, we collated three independent data sets with temporal information for at least one population: To test whether these fragments contain a molecular clock signal, we estimated the root-to-tip divergence using Path-o-gen v.1.4 (http://tree.bio.ed. ac.uk/software/pathogen/) to estimate how much genetic variation can be explained by the sampling date. We constructed maximum likelihood phylogenetic trees without the assumption of a molecular clock in Phylip v. 3.695 (evolution.genetics.washing ton.edu; Felsenstein, 1989) and tested whether the regression between root-to-tip distance in these maximum likelihood trees and the age of the samples indicated a clock-like signal. In addition, we tested for a significant temporal signal by randomising the temporal information across each data set 100 times and compared the resulting random evolutionary rates from BEAST with the real data set. A temporal signal is supported if there is a significant difference between the real data set and the randomised data sets (Ramsden et al., 2009; Alizon and Fraser, 2013) . Both analyses support a temporal signal in these data sets (Supplementary Figure S3 and Supplementary Table S4 ).