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1. Introduction
2. All pathogenic microorganisms
3. Between recombination and clonality
4. Main publications
5. Goal (1)
6. There is always a common denominator
7. Neo-Pasteurian era
8. Looking for the common denominator (1)
9. Looking for the common denominator (2)
10. Common denominator among pathogens
11. Clonal evolution restrained genetic recombination
12. Clonality definition
13. PCE = salami slicing model
14. No PCE – frequent recombination
15. Predominant clonal evolution
16. Recombinational load
17. The PCE concept
18. A gynogenetic fish that mates, but is clonal
19. Recombination does not break the PCE pattern
20. 3 main (linked) manifestations
21. Linkage disequilibrium: restrained recombination
22. Near-clading: what is it?
23. Congruence parameters
24. Clonality threshold
25. Different names given to microbe genetic clusters
26. Near-clade
27. Paleo-data mining
28. Caution with population genetics tests
29. “Evolutionary twins”
30. Parity between phylogenetic trees (1)
31. Multilocus Sequence Typing (MLST)
32. Giardia: “assemblages” and “subassemblages”
33. T. gondii isolates comprise six major clades
34. The Cryptococcus neoformans complex
35. E. coli - the “bacterial evolutionary twin” of T. cruzi
36. Animal and human pathogenic E. coli strains
37. Second step: the “Russian doll” model
38. Slicing of salami slicing model
39. The “Russian doll” model (1)
40. The “Russian doll” model (2)
41. Parity between phylogenetic trees (2)
42. Lesser near-clades Within T. cruzi near-clade 1
43. The “Russian doll” model (3)
44. Micro-clustering within the S. typhi H58 clade
45. Neisseria meningitidis is structured into clades
46. Near-clades are observed in Leishmania donovani
47. Viruses and clonality
48. Dengue virus: Katzelnick et al., 2016
49. Practical implications of the PCE approach
50. Goal (2)
51. The clonet concept
52. Example 1
53. Example 2
54. Revisiting the phylogenetic species concept (1)
55. Revisiting the phylogenetic species concept (2)
56. Applying the PCE approach to a given species (1)
57. Applying the PCE approach to a given species (2)
58. Contact details

Topics Covered

• Recombination vs. clonality
• Neo-Pasteurian era
• Looking for the common denominator among parasitic protozoa, fungi, bacteria and viruses
• PCE = salami slicing model
• No PCE – frequent recombination: soup model
• Recombinational load
• The PCE concept
• Linkage disequilibrium: restrained recombination
• Near-clading
• Parity between phylogenetic trees
• Multilocus Sequence Typing (MLST)
• The “Russian doll” model
• Practical implications of the PCE approach
• The clonet concept
• Revisiting the phylogenetic species concept (PSC)
• Applying the PCE approach to a given species

Links

Series:

• Using Bioinformatics in the Exploration of Genetic Diversity

Categories:

• Genetics & Epigenetics
• Methods
• Microbiology

Therapeutic Areas:

• Infectious Diseases

Talk Citation

Publication History

• Published on October 1, 2007
• Updated on April 30, 2018

Financial Disclosures

• Dr. Michel Tibayrenc has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.