Genomic and phenotypic parallelism during experimental evolution in different environments

We investigated the relationship between genomic and phenotypic evolution among replicate populations of Escherichia coli evolved for 1000 generations in four different environments. By re-sequencing evolved genomes, we identified environment- and population-specific mutational changes, as well as parallel changes in genes encoding transcription regulators. Parallel changes at the level of specific genes had different allelic patterns, depending on both the evolution environment and the particular mutated gene. Moreover, we could infer the theoretical number of beneficial alleles in spoT, one of the genes repeatedly targeted by mutations. Based on growth and fitness traits, evolved clones displayed parallel phenotypic adaptation to their respective evolution environments and parallel correlated responses measured across the three alternative environments. Among clones isolated from replicate populations evolved in the same environment, phenotypic parallelism was high whether or not the clones had parallel genetic changes, suggesting that mutations in different genes had similar pleiotropic effects. By contrast, when we compared clones isolated from populations evolved in different environments, clones that shared some mutated genes tended to have more parallel correlated responses, indicating that epistatic interactions do not entirely mask the effects of individual mutations. Together this work demonstrates both opportunities and limitations of predicting phenotypic responses from knowledge of organism genotypes.