Time-scaled phylogenetic tree reconstruction using BEAST

To reconstruct the temporal and spatial dynamics of CRF55_01B strain in various provinces, we performed a Bayesian discrete phylogeographic approach to estimate the rate of evolution and the time to the most recent common ancestor (tMRCA) using Markov chain Monte Carlo (MCMC) runs of 200 million generations with BEAST v1.8.4 [17] under a Bayesian Skygrid demographic model [18]. The final data set was analyzed using a general time-reversible (GTR) nucleotide substitution model [19] specifying a gamma distribution as a prior on each relative substitution rate and a relaxed uncorrelated lognormal (UCLN) molecular clock model to infer the timescale of HIV-1 evolution with a gamma distribution prior on the mean clock rate (shape = 0.001, scale = 1000) [20,21]. The Bayesian MCMC output was analyzed using Tracer v1.6 [22]. The Effective Sample Size (ESS) values for estimates were more than 200. Using LogCombiner (in BEAST package), we subsampled the posterior distribution of phylogenetic trees to generate an empirical distribution of 2000 trees representative of the posterior sample. The first 10%–30% of the states from each run were discarded as burn-in. Trees were summarized as maximum clade credibility (MCC) trees using TreeAnnotator (in BEAST package) and then visualized in FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree). SpreaD3 v0.9.7.1 [23] was used to draw the CRF55_01B propagation roadmap.