Open Access Highly Accessed Research article

Obscured phylogeny and possible recombinational dormancy in Escherichia coli

Shana R Leopold123, Stanley A Sawyer4, Thomas S Whittam5 and Phillip I Tarr1*

Author Affiliations

1 Department of Pediatrics, Washington University School of Medicine, Saint Louis, USA

2 Molecular Microbiology and Microbial Pathogenesis Program, Washington University School of Medicine, Saint Louis, USA

3 Institute of Hygiene, University of Muenster, Muenster, Germany

4 Department of Mathematics, Washington University, St. Louis, USA

5 Microbial Evolution Laboratory, National Food Safety and Toxicology Center, Michigan State University, East Lansing, USA

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BMC Evolutionary Biology 2011, 11:183  doi:10.1186/1471-2148-11-183

Published: 27 June 2011



Escherichia coli is one of the best studied organisms in all of biology, but its phylogenetic structure has been difficult to resolve with current data and analytical techniques. We analyzed single nucleotide polymorphisms in chromosomes of representative strains to reconstruct the topology of its emergence.


The phylogeny of E. coli varies according to the segment of chromosome analyzed. Recombination between extant E. coli groups is largely limited to only three intergroup pairings.


Segment-dependent phylogenies most likely are legacies of a complex recombination history. However, E. coli are now in an epoch in which they no longer broadly share DNA. Using the definition of species as organisms that freely exchange genetic material, this recombinational dormancy could reflect either the end of E. coli as a species, or herald the coalescence of E. coli groups into new species.

Definition of Species; Phylogeny; Recombination