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 reflect 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.

Figure 1

Phylogenies for clones from two evolving populations of E. coli, rooted by using the actual ancestral genotype. Phylogenies were inferred by parsimony (6) from RFLP data obtained using IS elements as probes. Notation indicates the generation at which each clone was sampled, followed by an arbitrary number to distinguish clones from the same sample. Clones in the box with the ancestor were identical to the ancestor on the basis of their IS fingerprints. Arrows mark some of the pivotal mutations that were shared by all clones in every later sample. (A) Population Ara+1. (B) Population Ara−1.

Figure 2

Trajectory of the average genetic distance between two evolving populations and their common ancestor, calculated as the number of genomic changes detected using IS elements as probes. Solid circles, solid line: Population Ara−1. Open squares, dashed line: Population Ara+1.

Figure 3

Trajectory of the average genetic diversity within two evolving populations, as calculated from all pairwise genetic distances. Solid circles, solid line: Population Ara−1. Open squares, dashed line: Population Ara+1.

Figure 4

Comparison between mutator (n = 3) and nonmutator (n = 9) populations of the average genetic distance from the common ancestor after 10,000 generations. Distances indicate the number of genomic changes detected using IS elements as probes. Error bars indicate 95% confidence intervals.