Although bacterial species display wide variation in their overall GC contents, the
genes within a particular species' genome are relatively similar in base composition.
As a result, sequences that are novel to a bacterial genome-i.e., DNA introduced through
recent horizontal transfer-often bear unusual sequence characteristics and can be
distinguished from ancestral DNA. At the time of introgression, horizontally transferred
genes reflect the base composition of the donor genome; but, over time, these sequences
will ameliorate to reflect the DNA composition of the new genome because the introgressed
genes are subject to the same mutational processes affecting all genes in the recipient
genome. This process of amelioration is evident in a large group of genes involved
in host-cell invasion by enteric bacteria and can be modeled to predict the amount
of time required after transfer for foreign DNA to resemble native DNA. Furthermore,
models of amelioration can be used to estimate the time of introgression of foreign
genes in a chromosome. Applying this approach to a 1.43-megabase continuous sequence,
we have calculated that the entire Escherichia coli chromosome contains more than
600 kb of horizontally transferred, protein-coding DNA. Estimates of amelioration
times indicate that this DNA has accumulated at a rate of 31 kb per million years,
which is on the order of the amount of variant DNA introduced by point mutations.
This rate predicts that the E. coli and Salmonella enterica lineages have each gained
and lost more than 3 megabases of novel DNA since their divergence.