Fig. 1

Clone phylogenies. Phylogenies depicting relationships among sequenced clones isolated from chemostats when allelic diversity attained its maximum; a chemostat 1, b chemostat 2, c chemostat 3. Distributions of different malK, malT, fimH, hfq, and opgH alleles are indicated by colored bars. For each gene, all alleles observed in the dataset are numbered (see Additional file 3: Table S6 for details of which number corresponds to which allele for each gene). Underlined numbers denote alleles independently observed in more than one chemostat, while numbers marked with an asterisk appear to have arisen more than once within the same vessel. Gray shading delineates clades comprised of clones that have not acquired the standard mutations related to enhanced glucose uptake and instead carry variant fimH alleles that contribute to biofilm formation. Bracketed clones in chemostat 3 exhibited mutations expected to revert the ancestral nonsense mutations in the housekeeping gene encoding sigma factor RpoD