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 generate a genome-wide estimate for the evolutionary rate in DWV, we calculated the mean of the relaxed clock means for the individual fragments (lp-fragment: 9.097 × 10 − 4 (95% highest posterior density: 4.412 × 10 − 4 -1.394 × 10 − 3 ), capsidfragment: 1.845 × 10 − 3 (1.159 × 10 − 3 -2.569 × 10 − 3 ), RdRp-fragment: 1.278 × 10 − 3 (4.131 × 10 − 4 -2.513 × 10 − 3 ), resulting in a mean evolutionary rate of 1.346 × 10 − 3 (5.41 × 10 − 4 -2.627 × 10 − 3 ) substitutions/site/year. We implemented this evolutionary rate as an uncorrelated lognormal clock prior for the DWV-subtype analysis with a lognormal distribution with a mean of 1.35 × 10 − 3 in real space and a log s.d. of 0.4. We used the default priors in BEAST v.1.8.1. We ran models with 2 runs each of 50 million MCMC generations, sampling every 5000 generations with a burn-in of 5 million generations to obtain effective sample sizes 4200. We examined traces for convergence using Tracer v.1.6 (http://www.tree.bio.ed.ac.uk/software/ tracer/) and used TreeAnnotator v.1.8 (beast.bio.ed.ac. uk/downloads) to produce a Maximum Clade Credibility tree for the DWV-subtype analysis. We used the method from Xia et al. (2003) , as implemented in DAMBE, to confirm that the alignment had not reached substitution saturation.