Figure 6: Host genetics influences the genetic basis of E. coli adaptation in the gut.

Frequencies of haplotypes in E. coli populations evolved in the gut of Rag2^−/− mice for 24 days. Clones (n∼20) isolated from the last day of evolution of lineages R1.1 to R1.15 (Fig. 1b) were screened for the presence of mutations previously identified in WT animals: gat phenotype (green), insertions in the regulatory region of focA (red) and dcuB (blue) and SNPs in the coding region of srlR (orange). Clones in which none of these mutations were found are shown in grey. Clonal interference is detected by the competition between clones carrying different beneficial mutations (stripes of different colours represent double mutants and clones carrying three mutations are shown as a checkered pattern).