Figure 2. Comparisons of barcode distributions in animals with or without clonal expansion events.

(A) CFU from the left half of the spleen 5 days post infection (dpi); points with the same fill and border color are derived from the same animal. (B, C) The underlying barcode distribution found in animals B and C are shown in the respective graphs on the right. The highly increased bacterial burden in animal B relative to animal C can be attributed to both a wider bottleneck and clonal expansion. In the barcode frequency distribution shown in (B), a diverse population is evident, as is the clear expansion of a few clones (arrows). In contrast, in animal C, N_b and N_r are similar to CFU, suggesting that the population has undergone relatively little replication. (D) N_b and N_r plots from the right lobe of the liver 1 dpi. The underlying barcode distributions in animals E, F, G, and H are shown in the respective graphs to the right (in E–H). Animals E and G have clonal expansion events; expansion is so substantial in (G) (~98% of reads) that the algorithm cannot distinguish the underlying population from noise, and N_r is not substantially higher than N_b for this sample. In contrast, N_r can identify this population in sample E. Red and blue lines denote subpopulations and noise, as in Figure 1.

Figure 2—figure supplement 1. Clonal expansion in the kidney.

(A) CFU of the right kidney is shown and is taken from the larger data set in Figure 1—figure supplement 4. Points with the same fill and border color are derived from the same animal; in animal B, the right kidney possessed 10,000 times more bacteria than the left kidney, which was sterile. (B) The underlying barcode distribution found in animal B. High CFU in the right kidney is attributable to marked expansion of eight cells.