  The ~4-Mbp basic genome shared by 32 independent isolates of E. coli
representing considerable population diversity has been approximated by
whole-genome multiple-alignment and computational filtering designed to remove
mobile elements and highly variable regions. Single nucleotide polymorphisms
(SNPs) in the 496 basic-genome pairs are identified and clonally inherited
stretches are distinguished from those acquired by horizontal transfer (HT) by
sharp discontinuities in SNP density. The six least diverged genome-pairs each
have only one or two HT stretches, each occupying 42-115-kbp of basic genome
and containing at least one gene cluster known to confer selective advantage.
At higher divergences, the typical mosaic pattern of interspersed clonal and HT
stretches across the entire basic genome are observed, including likely
fragmented integrations across a restriction barrier. A simple model suggests
that individual HT events are of the order of 10-kbp and are the chief
contributor to genome divergence, bringing in almost 12 times more SNPs than
point mutations. As a result of continuing horizontal transfer of such large
segments, 400 out of the 496 strain-pairs beyond genomic divergence of share
virtually no genomic material with their common ancestor. We conclude that the
active and continuing horizontal transfer of moderately large genomic fragments
is likely to be mediated primarily by a co evolving population of phages that
distribute random genome fragments throughout the population by generalized
transduction, allowing efficient adaptation to environmental changes.

Populations and Evolution;Biological Physics;Genomics;Quantitative Methods