Fig. 1.

Muller plots of medium bottleneck evolution. The Muller plots depict the evolutionary trajectory of medium bottleneck lineages 4 (A) and 7 (B). Frequencies and linkage of mutations were determined from population sequencing of individual selection steps (supplementary table S2, Supplementary Material online) and final clones (supplementary table S4, Supplementary Material online). The colors indicate the class into which mutations were sorted (target, efflux, or transcription/translation). A hatched pattern overlaying a color indicates the inferred presence (from sequencing data, linkage, or MIC) of a class of mutations in the population, but without any individual mutation rising above the 5% threshold for identification. Solid black lines indicate lineages which survived and were identified in the final culture, whereas dotted white lines indicate lineages that went extinct during the selection. For the lineages that became extinct during selection, where the linkage of mutations for constructing the figure was inferred, the data in supplementary tables S2 and S4, Supplementary Material online, should be considered authoritative.