Detection of recombination among Salmonella enterica strains using the incongruence length difference test

Molecular Phylogenetics and Evolution

Volumn 24, Issue 1, 2002, Pages 102-120

  Brown, Eric W ^a   Kotewicz, Michael L ^a   Cebula, Thomas A ^a  

^a CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASES; ADHESINS, BACTERIAL; BACTERIAL PROTEINS; DNA-BINDING PROTEINS; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; MODELS, GENETIC; MUTS DNA MISMATCH-BINDING PROTEIN; PHYLOGENY; RECOMBINATION, GENETIC; SALMONELLA ENTERICA; VIRULENCE;

BACTERIA (MICROORGANISMS); SALMONELLA; SALMONELLA ENTERICA;

EID: 0036375811     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(02)00222-1     Document Type: Article

References (71)

1. Congruence among mammalian mitochondrial genes
2. Split decomposition: A new and useful approach to phylogenetic analysis of distance data
3. Nucleotide sequence 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
4. Analysis of the type 1 pilin gene cluster fim in Salmonella: Its distinct evolutionary histories in the 5′ and 3′ regions
5. Comparative genetics of the inv-spa invasion complex of Salmonella enterica
6. Molecular genetic basis of allelic polymorphism in malate dehydrogenase (mdh) in natural populations of Escherichia coli and Salmonella enterica
7. Salmonella reference collection B (SARB): Strains of 37 serovars of subspecies I
8. Molecular genetic relationships of the salmonellae
9. The three R's of bacterial evolution: How replication, repair, and recombination frame the origin of species
10. Phylogenetic evidence for horizontal transfer of mutS alleles among naturally occurring Escherichia coli strains
11. Partitioning and combining characters in phylogenetic analysis
12. Hypermutability and homeologous recombination: Ingredients for rapid evolution
13. DNA repair and mutators: Effects on antigenic variation and virulence of bacterial pathogens
14. Mutator bacteria and resistance development
15. Weighting, partitioning, and combining characters in phylogenetic analysis
16. Phylogenetic relationships of Salmonella based on DNA sequence comparison of atpD encoding the beta subunit of ATP synthase
17. The location of four fimbrin-endoding genes, agfA, fimA, sefA, and sefD, on the Salmonella enteriditis and/or S. typhimurium XbaI-BlnI genomic restriction maps
18. Evolutionary implications of the frequent horizontal transfer of mismatch repair genes
19. A comprehensive set of sequence analysis programs for the VAX
20. Recombination in Escherichia coli and the definition of biological species
21. The logical basis of phylogenetic analysis
22. The retention index and the rescaled consistency index
23. Parsimony jackknifing outperforms neighbor-joining
24. Testing significance of incongruence
25. Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences
26. Confidence limits on phylogenies: An approach using the bootstrap
27. The consequences of growth of a mutator strain of Escherichia coli as measured by loss of function among multiple gene targets and loss of fitness
28. Cloning and molecular characterization of genes whose products allow Salmonella typhimurium to penetrate tissue culture cells
29. Type III secretion machines: Bacterial devices for protein delivery into host cells
30. The path to Salmonella
31. Horizontal transfer of a phosphatase gene as evidence for mosaic structure of the Salmonella genome
32. Nucleotide sequence mismatch of the Salmonella typhimurium mutS gene required for mismatch repair: Homology of mutS and hexA of Streptococcus pneumoniae
33. Altering the conserved nucleotide-binding motif in the Salmonella typhimurium MutS mismatch repair protein affects both its ATPase and mismatch binding activities
34. Pathogenicity islands and the evolution of microbes
35. Nontyphoidal salmonellosis
36. SplitsTree: Analyzing and visualizing evolutionary data
37. A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences
38. Host adaptation and the emergence of infectious disease: The Salmonella pathogen
39. Codon bias and base composition are poor indicators of horizontally transferred genes
40. Selfish operons: Horizontal transfer may drive the evolution of gene clusters
41. High mutation frequencies among Escherichia coli and Salmonella pathogens
42. Promiscuous origin of a chimeric sequence in the Escherichia coli O157:H7 genome
43. Detection of mutator subpopulations in Salmonella typhimurium LT2 by reversion of his alleles
44. Escherichia coli molecular phylogeny using the incongruence length difference test
45. The genus Salmonella
46. Designation of Salmonella enterica sp. nov., nom. rev., as the type and only species of the genus Salmonella
47. Recombinational basis of serovar diversity in Salmonella enterica
48. Relationship between evolutionary rate and cellular location among Inv/Spa invasion proteins of Salmonella enterica
49. Highly plastic chromosomal organization in Salmonella typhi
50. Gene trees in species trees
51. Analyzing the mosaic structure of genes
52. Evolutionary genetics of the proline permease gene (putP) and the control region of the proline utilization operon in populations of Salmonella and Escherichia coli
53. Intergeneric transfer and recombination of the 6-phosphogluconate dehydrogenase gene gnd in enteric bacteria
54. Size and sequence polymorphism in the isocitrate dehydrogenase kinase/phosphatase gene (aceK) and flanking regions in Salmonella enterica and Escherichia coli
55. Nucleotide polymorphism and evolution in the glyceraldehyde-3-phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli
56. Lateral gene transfer and the nature of bacterial innovation
57. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics
58. Evolution of evolvability
59. Clonal nature of Salmonella typhi and its genetic relatedness to other salmonellae as shown by multilocus enzyme electrophoresis, and proposal of Salmonella bongori comb
60. Parallel evolution of virulence in pathogenic Escherichia coli
61. Evolutionary genetics of Salmonella enterica
62. Statistical methods of DNA sequence analysis: Detection of intragenic recombination or gene conversion
63. Molecular evolution of the gnd locus of Salmonella enterica
64. The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
65. Selection against hypermutability in Escherichia coli during long term selection
66. Evolutionary genetics of the isocitrate dehydrogenase gene (icd) in Escherichia coli and Salmonella enterica