Bayesian phylogenetic analysis of partial CHIKV E1 gene sequences.

(A) Bayesian MCC tree of 249 Asian lineage strains calibrated to the sampling date and built using the HKY+G nucleotide substitution model, a lognormal relaxed clock and a Bayesian Skygrid coalescent model. Nodes with posterior probabilities (clade-credibility values) ≥0.9 have 95% HPD intervals for node heights shown. The two main epidemic Asian lineage clades (CL) are also shown. (B) A subtree of the American and Caribbean sublineage showing posterior probabilities and calibrated tMRCA and 95% HPD intervals for statistically supported monophyletic groups. For clarity, node bars with 95% HPD intervals are not shown, only relevant strains are labelled, and the colour code is as in section a).