Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures

Isolated populations derived from a common ancestor are expected to diverge genetically and phenotypically as they adapt to different local environments. To examine this process, 30 populations of Escherichia coli were evolved for 2,000 generations, with six in each of five different thermal regimes: constant 20 degrees C, 32 degrees C, 37 degrees C, 42 degrees C, and daily alternations between 32 degrees C and 42 degrees C. Here, we sequenced the genomes of one endpoint clone from each population to test whether the history of adaptation in different thermal regimes was evident at the genomic level. The evolved strains had accumulated 5.3 mutations, on average, and exhibited distinct signatures of adaptation to the different environments. On average, two strains that evolved under the same regime exhibited similar to 17% overlap in which genes were mutated, whereas pairs that evolved under different conditions shared only similar to 4%. For example, all six strains evolved at 32 degrees C had mutations in nadR, whereas none of the other 24 strains did. However, a population evolved at 37 degrees C for an additional 18,000 generations eventually accumulated mutations in the signature genes strongly associated with adaptation to the other temperature regimes. Two mutations that arose in one temperature treatment tended to be beneficial when testedintheothers, although less so than in the regime in which they evolved. These findings demonstrate that genomic signatures of adaptation can be highly specific, even with respect to subtle environmental differences, but that this imprintmay become obscured over longer timescales as populations continue to change and adapt to the shared features of their environments.