• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of jbacterPermissionsJournals.ASM.orgJournalJB ArticleJournal InfoAuthorsReviewers
J Bacteriol. Nov 1991; 173(22): 7257–7268.
PMCID: PMC209233

Recombination in Escherichia coli and the definition of biological species.

Abstract

The DNA sequence of part of the gnd (6-phosphogluconate dehydrogenase) gene was determined for eight wild strains of Escherichia coli and for Salmonella typhimurium. Since a region of the trp (tryptophan) operon and the phoA (alkaline phosphatase) gene have been sequenced from the same strains, the gene trees for these three regions were determined and compared. Gene trees are different from species or strain trees in that a gene tree is derived from a particular segment of DNA, whereas a species or strain tree should be derived from many such segments and is the tree that best represents the phylogenetic relationship of the species or strains. If there were no recombination in E. coli, the gene trees for different genes would not be statistically different from the strain tree or from each other. But, if the gene trees are significantly different, there must have been recombination. Methods are proposed that show these gene trees to be statistically different. Since the gene trees are different, we conclude that recombination is important in natural populations of E. coli. Finally, we suggest that gene trees can be used to create an operational means of defining bacterial species by using the biological species definition.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.9M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Achtman M, Mercer A, Kusecek B, Pohl A, Heuzenroeder M, Aaronson W, Sutton A, Silver RP. Six widespread bacterial clones among Escherichia coli K1 isolates. Infect Immun. 1983 Jan;39(1):315–335. [PMC free article] [PubMed]
  • Achtman M, Pluschke G. Clonal analysis of descent and virulence among selected Escherichia coli. Annu Rev Microbiol. 1986;40:185–210. [PubMed]
  • Bisercić M, Feutrier JY, Reeves PR. Nucleotide sequences of the gnd genes from nine natural isolates of Escherichia coli: evidence of intragenic recombination as a contributing factor in the evolution of the polymorphic gnd locus. J Bacteriol. 1991 Jun;173(12):3894–3900. [PMC free article] [PubMed]
  • Brenner DJ, Falkow S. Genetics of the Enterobacteriaceae. C. Molecular relationships among members of the Enterobacteriaceae. Adv Genet. 1971;16:81–118. [PubMed]
  • DuBose RF, Dykhuizen DE, Hartl DL. Genetic exchange among natural isolates of bacteria: recombination within the phoA gene of Escherichia coli. Proc Natl Acad Sci U S A. 1988 Sep;85(18):7036–7040. [PMC free article] [PubMed]
  • DuBose RF, Hartl DL. The molecular evolution of bacterial alkaline phosphatase: correlating variation among enteric bacteria to experimental manipulations of the protein. Mol Biol Evol. 1990 Nov;7(6):547–577. [PubMed]
  • Hartl DL, Dykhuizen DE. The population genetics of Escherichia coli. Annu Rev Genet. 1984;18:31–68. [PubMed]
  • Jiang XM, Neal B, Santiago F, Lee SJ, Romana LK, Reeves PR. Structure and sequence of the rfb (O antigen) gene cluster of Salmonella serovar typhimurium (strain LT2). Mol Microbiol. 1991 Mar;5(3):695–713. [PubMed]
  • Jin L, Nei M. Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol Biol Evol. 1990 Jan;7(1):82–102. [PubMed]
  • Lawrence JG, Dykhuizen DE, DuBose RF, Hartl DL. Phylogenetic analysis using insertion sequence fingerprinting in Escherichia coli. Mol Biol Evol. 1989 Jan;6(1):1–14. [PubMed]
  • Levin BR. Periodic selection, infectious gene exchange and the genetic structure of E. coli populations. Genetics. 1981 Sep;99(1):1–23. [PMC free article] [PubMed]
  • Milkman R. Electrophoretic variation in Escherichia coli from natural sources. Science. 1973 Dec 7;182(4116):1024–1026. [PubMed]
  • Milkman R, Bridges MM. Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics. 1990 Nov;126(3):505–517. [PMC free article] [PubMed]
  • Milkman R, Crawford IP. Clustered third-base substitutions among wild strains of Escherichia coli. Science. 1983 Jul 22;221(4608):378–380. [PubMed]
  • Nasoff MS, Baker HV, 2nd, Wolf RE., Jr DNA sequence of the Escherichia coli gene, gnd, for 6-phosphogluconate dehydrogenase. Gene. 1984 Mar;27(3):253–264. [PubMed]
  • Nasoff MS, Wolf RE., Jr Molecular cloning, correlation of genetic and restriction maps, and determination of the direction of transcription of gnd of Escherichia coli. J Bacteriol. 1980 Aug;143(2):731–741. [PMC free article] [PubMed]
  • Nei M, Stephens JC, Saitou N. Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes. Mol Biol Evol. 1985 Jan;2(1):66–85. [PubMed]
  • Ochman H, Selander RK. Standard reference strains of Escherichia coli from natural populations. J Bacteriol. 1984 Feb;157(2):690–693. [PMC free article] [PubMed]
  • Ochman H, Selander RK. Evidence for clonal population structure in Escherichia coli. Proc Natl Acad Sci U S A. 1984 Jan;81(1):198–201. [PMC free article] [PubMed]
  • Ochman H, Whittam TS, Caugant DA, Selander RK. Enzyme polymorphism and genetic population structure in Escherichia coli and Shigella. J Gen Microbiol. 1983 Sep;129(9):2715–2726. [PubMed]
  • Orskov F, Orskov I. From the national institutes of health. Summary of a workshop on the clone concept in the epidemiology, taxonomy, and evolution of the enterobacteriaceae and other bacteria. J Infect Dis. 1983 Aug;148(2):346–357. [PubMed]
  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. [PubMed]
  • Sawyer S. Statistical tests for detecting gene conversion. Mol Biol Evol. 1989 Sep;6(5):526–538. [PubMed]
  • Sawyer SA, Dykhuizen DE, DuBose RF, Green L, Mutangadura-Mhlanga T, Wolczyk DF, Hartl DL. Distribution and abundance of insertion sequences among natural isolates of Escherichia coli. Genetics. 1987 Jan;115(1):51–63. [PMC free article] [PubMed]
  • Sawyer SA, Dykhuizen DE, Hartl DL. Confidence interval for the number of selectively neutral amino acid polymorphisms. Proc Natl Acad Sci U S A. 1987 Sep;84(17):6225–6228. [PMC free article] [PubMed]
  • Sharp PM, Li WH. The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol Biol Evol. 1987 May;4(3):222–230. [PubMed]
  • Sharp PM, Li WH. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987 Feb 11;15(3):1281–1295. [PMC free article] [PubMed]
  • Smith JM, Dowson CG, Spratt BG. Localized sex in bacteria. Nature. 1991 Jan 3;349(6304):29–31. [PubMed]
  • Sourdis J, Nei M. Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. Mol Biol Evol. 1988 May;5(3):298–311. [PubMed]
  • Stoltzfus A, Leslie JF, Milkman R. Molecular evolution of the Escherichia coli chromosome. I. Analysis of structure and natural variation in a previously uncharacterized region between trp and tonB. Genetics. 1988 Oct;120(2):345–358. [PMC free article] [PubMed]
  • Whittam TS, Ochman H, Selander RK. Multilocus genetic structure in natural populations of Escherichia coli. Proc Natl Acad Sci U S A. 1983 Mar;80(6):1751–1755. [PMC free article] [PubMed]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

Formats:

Related citations in PubMed

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...