We used a combination of genomic techniques to monitor chromosomal evolution across hundreds of generations as Escherichia coli adapted to growth-limiting concentrations of either lactulose, methyl-galactoside, or a 72:28 mixture of the two. DNA microarrays identified 8 unique duplications and 16 unique deletions among 42 evolvants from 23 chemostat experiments. Each mutation was confirmed by sequencing PCR-amplified flanking genomic DNA and, except for one deletion, an insertion sequence was found at the break point. vPCR of insertion sequences identified these same mutations and 16 additional insertions (all confirmed by sequencing). The pattern of genomic evolution is highly reproducible. Statistical analyses show that duplications at lac and mutations in mgl are adaptations specific to lactulose and to methyl-galactoside, respectively. Adaptation to mixed sugars is characterized by similar mutations, but lac duplications and mgl mutations usually arise in different backgrounds, producing ecological specialists for each sugar. This suggests that an antagonistic pleiotropic tradeoff between duplications at lac and mutations in mgl retards the evolution of generalists. Other mutations that repeatedly appear in replicate experiments are adaptations to the chemostat environment and are not specific to one or the other sugar.W e have taken advantage of the repeatability of laboratory adaptation to investigate the roles of insertion sequences (IS) in the evolution of resource specialization.The repeatability of laboratory adaptation is well documented (1-11) and is perhaps attributable to using large populations with simple ecologies. Large populations reduce the role of chance in evolution: random genetic drift is minimized, whereas mutation, always erratic in small populations, produces numerous allelic variants with each generation. In simple constant environments, selection becomes focused with great intensity on a few key genes. This makes experimental evolution far more reproducible than typically envisioned for small populations inhabiting complex natural environments (12). Reproducibility makes possible rigorous tests of adaptive hypotheses. For example, Cooper et al. (13) used DNA expression macroarrays to identify parallel changes in the expression profiles of two evolvants. Guided by the observation that many of the genes with changed expression belong to the ppGpp and CRP regulons, they identified a mutation in spoT in one population that, when reintroduced into the ancestral genetic background, increased fitness as well as reproducing many of the changes in expression.IS elements are small (1-to 2-kb) segments of DNA capable of transposing within and between prokaryotic replicons (14). A major source of insertional mutations and chromosomal rearrangements (15), their evolutionary significance is a subject of perennial interest (16)(17)(18)(19)(20). Patterns of sequence polymorphism among natural isolates of Escherichia coli suggest a brisk turnover of elements (21), with both the numbers and location...