Extended Data Figure 5. Evidence for within-host cladal structure.

A. Pairwise distances between samples measured using the all-locus distance metric plotted against pairwise distances in time (measured in days) between samples being collected. Internal distances between samples in the proposed main clade are shown in black, distances between samples in the main clade and samples collected on days 93 and 95 are shown in red, and internal distances between samples collected on days 93 and 95 are shown in green. B. Pairwise distances between samples in the larger clade (black) and between these samples and those collected on days 93 and 95 (red). The median values of the distributions of these values are significantly different according to a Mann Whitney test. C. Pairwise distances between samples in the main clade, once those collected on days 86, 89, 93, 95 have been removed (black) and between these samples and those collected on days 86 and 89 (red). The median values of the distributions of these values are not significantly different at the 5 level according to a Mann Whitney test.