  Martincorena et al. estimated synonymous diversity ({\theta}s = 2N{\mu})
across 2,930 orthologous gene alignments from 34 Escherichia coli genomes, and
found substantial variation among genes in the density of synonymous
polymorphisms. They argue that this pattern reflects variation in the mutation
rate per nucleotide ({\mu}) among genes. However, the effective population size
(N) is not necessarily constant across the genome. In particular, different
genes may have different histories of horizontal gene transfer (HGT), whereas
Martincorena et al. used a model with random recombination to calculate
{\theta}s. They did filter alignments in an effort to minimize the effects of
HGT, but we doubt that any procedure can completely eliminate HGT among closely
related genomes, such as E. coli living in the complex gut community.
  Here we show that there is no significant variation among genes in rates of
synonymous substitutions in a long-term evolution experiment with E. coli and
that the per-gene rates are not correlated with {\theta}s estimates from genome
comparisons. However, there is a significant association between {\theta}s and
HGT events. Together, these findings imply that {\theta}s variation reflects
different histories of HGT, not local optimization of mutation rates to reduce
the risk of deleterious mutations as proposed by Martincorena et al.
