Fig. 1

Recombination map of the canine distemper virus (CDV) H gene in strains of the 188-sequence data set. For each recombination event, the left side of the figure shows (a) the BOOTSCAN plot, and the second panel shows (b) the similarity plot. The y-axis shows (a) the percentage of permutation trees and (b) the pairwise identity of each pair in the sequence. The x-axis is the alignment position. The analysis was performed with a sliding window of 200 nt with a 20-nt step. The comparison was performed using 50 % consensus sequences with 1000 bootstrap replicates. Each curve in the figure compares the query and reference sequences. Both plots were generated with the Simplot program. Potential recombination breakpoints are identified where sudden alterations in bootstrap values or in similarity values occurred or where crossover occurred. Potential recombination breakpoints are identified where sudden alterations in bootstrap or similarity values occurred or where a crossover occurred. The third panel (c) shows a schematic diagram of potential recombinant regions and breakpoint locations identified by Recombination Detection Program v3.44 (RDP). Phylogenetic trees were compared by neighbor sequence fragment alignments flanking the breakpoint. (d). The potential recombinant strains, major parent strains, minor parent strains, and non-parent strains are indicated in red, blue, green, and purple, respectively