Fig. 3

Evolutionary analysis of HPyV9 genomes by the Maximum Likelihood method (panel a), haplotype network of HPyV9 genomes (panel b) and NCCR sequences (panel c). The evolutionary history was inferred by using the Maximum Likelihood method and Tamura-Nei model⁶⁴. The tree with the highest log likelihood (-7517.08) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Tamura-Nei model, and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site (next to the branches). This analysis involved 7 nucleotide sequences. Codon positions included were 1st + 2nd + 3rd + Noncoding. There were a total of 5105 positions in the final dataset. Evolutionary analyses were conducted in MEGA X⁶⁵, and TCS networks were developed by PopART⁶⁶. In TCS network, the size of the circle representing a haplotype is relative to the number of sequences. Tables show the GenBank accession numbers of the sequences for each haplotype. NCCR: noncoding control region.