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 determine the appropriate molecular clock models for each data set, we used the path sampling maximum likelihood estimator implemented in BEAST 1.8 (Baele et al., 2012 (Baele et al., , 2013 . As this method is very computationally intensive, we first used a range of simpler tests to limit the number of models to be compared by this method as suggested by Alizon and Fraser (2013) , and Drummond and Bouckaert (2014) . For the three large temporal data sets, we used jModelTest v.2.1.1 (https://github.com/ ddarriba/jmodeltest2; Posada, 2008) to compare substitution models based on the Bayesian Information Criterion (Alizon and Fraser 2013) ; the resulting substitution models were the Tamura-Nei (TnR) model (lp-fragment) and the Hasegawa, Kashino and Yano (HKY) model (vp3-and RdRp-fragments), both with Gamma variation. For the DWV-subtype data set, we compared the general time-reversible model and the SRD06 model (Shapiro et al., 2006) using path sampling. We partitioned substitution rates between the first and second and third codon positions as, for all data sets, the third codon position had a significantly higher rate. We tested whether a strict clock rate can be excluded by running models with a lognormal relaxed clock; if the relaxed clock's coefficient of variation statistic abuts the zero boundary, a strict clock cannot be excluded (Gray et al., 2011) . We ran models with exponential population growth for all models; if the exponential growth rate was significantly higher than zero, a constant population size can be excluded. We then used path sampling to distinguish between clock models (exponential and lognormal relaxed clock) and demographic models (constant population size, exponential population growth or a Gaussian Markov random field (GMRF skyride); Drummond et al., 2002; Minin et al., 2008) as indicated for each fragment by the initial analyses. Based on these analyses, we chose an exponential relaxed clock and exponential growth prior for the lp-and capsid-fragments and a lognormal relaxed clock and constant growth prior for the RdRpfragment as well as for the DWV-subtype analyses.