Figure 3

The quasispecies formed during the evolution of lineage 6L. As in lineage 6H, different clouds are formed in each burst evaluated: (A) burst 22; (B) burst 23; (C) burst 39; and (D) burst 42. The master sequence names are given according to their order of appearance, as a continuation of the numbering in lineage A. Note that the genotype of the MS3 appeared in the cloud A35 at low frequency, and that MS1 and MS2 are also recurrent from lineage 6H. Spheres represent mutants present at different frequencies denoted by their radii. The genetic relationships between the mutants and the MS are given by their Hamming distances. Only mutants that persist through various bursts or lineages are colored different than yellow, and the color is preserved throughout all the networks. Red spheres are calculated median vectors that represent either ancestral sequences or extant sequences not sampled. A different network outcome is formed from a consolidated alignment of all the sequences in the lineage (E).