Maximum likelihood phylogenetic trees were estimated with PAUP* 4.0 [62] using the general time reversible nucleotide substitution model specifying the proportion of invariant sites and a gamma distributed rate variation, which had been selected by MODELTEST [63], and tree-bisection-recombination branch-swapping.
The tree topology was fixed, the branch lengths estimated by PhyML were used as the initial values, and alignment gaps and ambiguous letters were removed for the ancestral sequence reconstruction, using the general time-reversible nucleotide substitution model (BASEML parameters: cleandata = 1, fix_blength = 1, model = 7).
Nucleotide sequences within a gene family were aligned with ClustalW v2.1 (Larkin et al. 2007), and an ML tree was constructed using RAxML v8.1.17 (Stamatakis 2014) using the general time reversible (GTR) nucleotide substitution model and gamma distribution pattern.
Phylogenetic evidence for recombination was tested for the genomic sequences using the split-decomposition method implemented in SPLITSTREE version 4.11.3 [30] using the general time reversible (GTR) scheme of substitution with a gamma distribution (Γ4) model of site rates variation (GTR + Γ4) (see below for a justification of this choice).
The analysis was performed by using the general time-reversible model of nucleotide substitution assuming an uncorrelated lognormal molecular clock (22 ).
We concatenated the alignments of genes present in all strains, and constructed a maximum-likelihood phylogeny with RaxML [ 33], using the General Time Reversible model of nucleotide substitution.
A phylogeny was also inferred by maximum likelihood (ML) as implemented in RAxML (Stamatakis et al. 2005), using the general time reversible (GTR) model of nucleotide substitution.
Bayesian coalescent analysis was performed in BEAST v1.6.1 to estimate the mean evolutionary rate of the E gene and the time to the most recent common ancestor (tMRCA) for the most prevalent group using the general time reversible (GTR) + gamma + I substitution model and the relaxed uncorrelated lognormal molecular clock [ 22].
The maximum-likelihood ratios then were calculated using the general time-reversible model with a gamma correction for site variation as the nucleotide substitution model.
