Genomic evolution during a 10,000-generation experiment with bacteria

Abstract

Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species. However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms. To overcome this limitation, we sampled genomes from populations of Escherichia coli evolving in the laboratory for 10,000 generations. We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach ref lect rearrangements (including transpositions) rather than point mutations. The evolving genomes became increasingly different from their ancestor over time. Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint after 10,000 generations. As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population. Certain pivotal mutations were shared by all descendants in a population, and these are candidates for beneficial mutations, which are rare and difficult to find. More generally, these data show that the genome is highly dynamic even over a time scale that is, from an evolutionary perspective, very brief.Our collaborative work builds on two previous studies. One examined genomic variation among cells recovered from populations of Escherichia coli that had been stored as a ''stab'' culture for Ϸ30 years without renewal of the medium and, hence, with little opportunity for growth (1, 2). A high level of diversity was found using restriction fragment length polymorphism (RFLP) analysis with eight insertion sequence (IS) elements as molecular probes. Clones differed from their putative ancestor by ϳ12 changes, on average. It was unclear, however, whether the prolonged starvation had an important role in promoting or maintaining this variability and whether the derived bacteria were any better adapted to the storage regime than was their ancestor.The other study examined the dynamics of phenotypic evolution in populations of E. coli that were propagated by daily serial transfer for 1,500 days, yielding 10,000 generations of binary fission (3, 4). The fitness of the bacteria improved by ϳ50%, on average, relative to the ancestor, and other phenotypic properties, such as cell size, also underwent large changes. The rate of phenotypic evolution was very fast during the initial 2,000 generations, but much slower during the subsequent 8,000 generations. However, certain other issues were not addressed, including the extent of genomic change and whether the rate of molecular evolution decelerated in parallel with phenotypic evolution. At one extreme, the derived genotypes may differ from their ancestor by only a small number of point mutations, which would require very extensive DNA sequencing to discover. At the other extreme, the derived lines may have undergon...

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