Fig 1.
Maximum likelihood phylogeny of 321 RABV sequences from five concatenated genes.
The major clades of RABV are indicated in boxes. The names of subclades and lineages defined for the Arctic-related, Asian and Cosmopolitan clades are detailed in S1 Table, with corresponding bootstrap values shown for major nodes. The tree is mid-point rooted for clarity only, and shows the division into bat-related RABV including the RAC-SK and bat clades, and dog-related RABV including the Africa-2, Africa-3, Arctic-related, Asian, Indian subcontinent and Cosmopolitan clades.
Fig 2.
Evolutionary rates of RABV genes in the dog-related group.
(A) Rates of nucleotide substitution per site, per year were estimated for each RABV gene: nucleoprotein (N), phosphoprotein (P), matrix (M), glycoprotein (G) and polymerase (L), for the concatenated non-coding regions (NC) and for the five concatenated RABV genes (5 genes). Both the mean and the 95% highest posterior density (HPD) values on the rate are shown. (B) Substitution rates in the N and G genes of the dog-related group RABV, a sub-set of RABV circulating in mongooses (MG) in Africa-3 clade and in the Caribbean, in ferret-badgers (FB) in Asia, and in dogs in Asia and Africa. Note the different y-axes (rates) in both cases.
Fig 3.
Maximum clade credibility phylogeny of 248 dog-related RABV utilizing five concatenated genes.
Tip times represent the time (year) of sampling. Bayesian estimates of divergence time are also shown. Upper and lower limits of the 95% highest posterior density (HPD) estimates and the posterior probability values are shown for major nodes.
Table 1.
Selection pressures in five genes from bat- and dog-related RABVs.