partition analysis of quasispecies (PAQ) applied to sequences derived from mutagenized FMDV populations. The initial biological clone of each passage series is depicted as a dot, with an initial intrapopulation average distance given arbitrarily the value AD = 0.0. The populations analyzed in A and B are those described in Figure 1A and Figure 1B, respectively. For simplicity, only the drug treatment (FU, 5-fluorouracil, green; AZC, azacytidine, blue; R, ribavirin, black; no drug, red), and the populations analyzed are depicted. The AD value was measured for each population considering no partition. Values are based on nucleotide sequences of the 3D(polymerase)-coding region, genomic residues 6609 to 8013 for A), and 6667 to 7997 for B), except for population RA0p35 for which residues 7150–7997 were used. For comparison, population RAp35 was also analyzed using residues 7150–7997; in that case the sphere is represented with a dotted line inside the large sphere. The diameter of each sphere is proportional to the AD value which is indicated next to each sphere. Procedures for nucleotide sequencing and PAQ analysis are described in Methods.