FIG 8.

Intraclade recombination analysis of clade 5. (A) Phylogenetic network based on the complete genomes of strains from clade 5. (B and C) Simplot analysis of arbitrarily selected putative recombinant strains from clade 5 to illustrate phylogenetic incongruences. Arrows highlight recombination crossovers supported by two or more mutations on each side of the crossover. (D) Recombinant strains from clade 5 suggested by the RDP program and statistical support yielded by each method for respective recombination event.