Maximum clade credibility phylogenetic tree based on 67 Arctic-related RABV N gene sequences.

<p>The horizontal branches are drawn to a scale of estimated year of divergence. Upper and lower limits of the 95% highest posterior density (HPD) estimates, and the corresponding divergence dates for the selected nodes are shown. Posterior probability values are shown above the branch for relevant key nodes only. Isolates for which the complete N gene sequence was obtained in this study are indicated by an asterisk.</p

A: Magnified phylogeny of the Indian subcontinent clade.

<p>B: Magnified phylogeny of the Arctic-like 1 and 3 sub-clades. Branches are labeled with bootstrap values generated with both the neighbor-joining (1,000 bootstrap replications) and maximum likelihood (100 bootstrap replications, number in brackets) algorithms. Bootstrap values are given for selected relevant nodes only. A scale indicating genetic distance is presented by the horizontal bar. Designations of the different RABV phylogroups (clade, sub-clade and lineage) are as indicated, based on previously defined assignments <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002560#pntd.0002560-Bourhy1" target="_blank">[5]</a>, <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002560#pntd.0002560-Kuzmin1" target="_blank">[25]</a>. Isolates for which the complete N gene sequence was obtained in this study are indicated by an asterisk with the viruses from Nepal underscored.</p

Clade specific amino acid differences in the nucleoprotein of Nepalese RABV.

a<p>Excludes virus sample 3878-10 which adopts Val at position 179.</p

Clade specific amino acid differences in the glycoprotein of Nepalese RABV.

a<p>Amino acid positions exclude the 19aa signal peptide sequence.</p>b<p>Virus samples 3878-09 and 3878-78 have the Indian subcontinent residue.</p>c<p>Virus samples 3878-09 and 3878-78 have Thr substitution.</p>d<p>Virus sample 3878-78 has the Indian subcontinent residue.</p

Maximum likelihood phylogenetic tree based on 173 complete RABV N gene nucleotide sequences.

<p>Branches are labeled with bootstrap values generated with both the neighbor-joining (1,000 bootstrap replications) and maximum likelihood (100 bootstrap replications, number in brackets) algorithms. Bootstrap values are given for selected relevant nodes only. A scale indicating genetic distance is presented by the horizontal bar. Designations of the different RABV phylogroups (clade, sub-clade and lineage) are as indicated, based on previously defined assignments <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002560#pntd.0002560-Bourhy1" target="_blank">[5]</a>, <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002560#pntd.0002560-Kuzmin1" target="_blank">[25]</a>. Isolates for which the complete N gene sequence was obtained in this study are indicated by an asterisk with the viruses from Nepal underscored.</p