phylogenetic analysis of individual molecular clones of FMDV populations passaged in the absence or presence of mutagens. The trees were constructed with sequences from the 3D (polymerase)-coding region (nucleotide residues 6609 to 8013; numbering of residues as in ) of molecular clones obtained from populations at passage 1 (left) or passage 25 (right) of FMDV C-S8c1in BHK-21 cells. The populations analyzed correspond to those depicted in Figure 1A. Each dot represents the sequence of an individual clone as follows: red, clones from the populations passaged in the absence of drug (no drug); green, clones from the populations passaged in the presence of 5-fluorouracil (FU); blue, clones from the populations passaged in the presence of 5-azacytidine (AZC). The central Sequence according to PAQ is indicated by an arrow. The NJ method, with the Kimura 2 parameter algorithm, and 1000 bootstrap resamplings were used. Bootstrap values were below 75, and values higher than 60 are indicated in parenthesis. The position of the consensus sequence of the corresponding populations is indicated with an asterisk. MARLS was included as an outgroup of the tree. The origin of the viruses, and procedures for clonal analysis and nucleotide sequence determination are detailed in Methods.