phylogenetic analysis of individual molecular clones of MARLS populations passaged in the absence or presence of ribavirin. Trees were constructed using the NJ method under Kimura 2-parameter model, with 1000 bootstrap resamplings. Bootstrap values higher than 75 are indicated with numbers; values between 60 and 74 are indicated in parenthesis. Each tree represents the analysis of one individual population from the MARLS lineage depicted in Figure 1B. Each population can be identified by the name of the corresponding consensus sequence indicated with an asterisk. Each dot represents the sequence of an individual molecular clone; red indicates absence of drug and black presence of ribavirin. The central Sequence according to PAQ is indicated by an arrow. A) Trees constructed with sequences from the 3D (polymerase)-coding region, residues 6667–7997, of FMDV. B) Comparison of the phylogenetic position of clones derived from populations RAp35 and RA0p35 (depicted in Figure 1); residues 7150–7997 from the 3D (polymerase)-coding were used. Procedures for clonal analysis and nucleotide sequencing are detailed in Methods.