Data from: Synonymous genetic variation in natural isolates of Escherichia coli does not predict where synonymous substitutions occur in a long-term experiment

Synonymous genetic differences vary by more than 20-fold among genes in
natural isolates of Escherichia coli. One hypothesis to explain this
heterogeneity is that genes with high levels of synonymous variation
mutate at higher rates than genes with low synonymous variation. If so,
then one would expect to observe similar mutational patterns in evolution
experiments. In fact, however, the pattern of synonymous substitutions in
a long-term evolution experiment with E. coli does not support this
hypothesis. In particular, the extent of synonymous variation across genes
in that experiment does not reflect the variation observed in natural
isolates of E. coli. Instead, gene length alone predicts with high
accuracy the prevalence of synonymous changes in the experimental
populations. We hypothesize that patterns of synonymous variation in
natural E. coli populations are instead caused by differences across
genomic regions in their effective population size that, in turn, reflect
different histories of recombination, horizontal gene transfer, selection,
and population structure.