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Species Populations Genotypes Valeria Souza & Luis Eguiarte

Species Populations Genotypes Valeria Souza & Luis Eguiarte. HGT. I.- Do species exist in bacteria , and what are their boundaries? II.-Which are the microevolutionary processes that lead to speciation in Bacteria ? III.-Which is the unit of selection ?.

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Species Populations Genotypes Valeria Souza & Luis Eguiarte

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  1. Species Populations Genotypes Valeria Souza & Luis Eguiarte HGT

  2. I.- Do species exist in bacteria, and what are their boundaries? II.-Which are the microevolutionary processes that lead to speciation in Bacteria? III.-Which is the unit of selection?

  3. I.- Do species exist in bacteria, and what are their boundaries?

  4. Bacterial species: traditional concept: similar things... i.e., phenotypic/genetic “clusters” Macrobial and microbial systematics split with Mayr’s Biological Species Concept (1944): organisms whose divergence is restricted by recombination (gene flow/ sex) between them. Ernest Mayr 1928

  5. Bacteria: “Modern” , similarity methods for recognition of species as clusters: 1) Phenotypic clusters. 2) DNA-DNA hybridization: 70%. 3) DNA sequence: 3% divergent in 16S rRNA Tech driven ideas...

  6. A circularity element in this empirical/similarity ideas... : Calibrate new molecular techniques to yield the clusters previously determined by phenotypic similarity criteria... May seem that bacterial systematics is in general lacking atheory-based concept of species.

  7. Dykhuizen & Green (1991): classify bacteria using the Biological Species Concept: Phylogenetic approach: sequence data to identify groups that have or not been exchanging genes. Lateral transfer is a problem for the biological concept.

  8. Cohesion Species Concept(Templeton, 1989): A species is a group of organisms whose divergence is restricted by one or more forces of cohesion. Hybridization can be considered. Useful in bacterial groups that form separate phenotypic clusters, despite recurrent recombination (Cohan, 2002),

  9. Sexual species: predominant cohesive force is the genetic exchange within the species. (Completely) Asexual species: according to Cohan, the predominant cohesive force in Bacteria is periodic selection. Divergence and future speciation occurs when a clone escapes from this cohesive force.

  10. Chromosome Plasmids Silva et al. 2003 Sympatric species in Rhizobium/ cohesive gene flow

  11. II.- Which are the microevolutionary processes that lead to speciation in Bacteria? or, How do bacteria break loose of the cohesion within the species?

  12. Diversification in bacteria (Lawrence, 1999) : 1) Point mutation: may allow selection to catalyze gradual niche expansion (climb a peak in the adaptive topography). 2) Horizontal transfer: may catapult an organism into an effective competitor or into a previous unexplored niche (reach new peaks in the a.t.).

  13. Two models: a) The clonal model (Cohan 2002): Mutation and periodic selection shape the population structure. Bacterial diversity is organized into discrete clusters, separated by gaps. These clusters are recognized as species.

  14. The clonal model (cont.) Ecotype: strains using the same or similar ecological resources. Periodic selection: without recombination, an adaptive mutant from within the ecotype out-competes to extinction all other strains of the same ecotype. Frederick M. Cohan, 2002, Annu. Rev. Microbiol. 56:457–87

  15. In the clonal model, Ecotypes can diverge very fast to separated species: Ergo: the number of bacterial species in the world is very large (i.e., may be100,000 to 1,000,000 in an environment...)

  16. b) Not so clonal model the cohesion of the gene pool of a species is maintained by gene flow within a gene pool and by selection that purges the recombinants between species. Speciation is not so fast . Ergo: The number of bacterial species is not so large (i.e., may be 100-1000 in each environment...).

  17. Species gene pool ecotypes within a geographic region sister species Genetic cohesion is a quantitative question see Claudia Silva poster Gogarten et al., 2002, Prokaryotic evolution in light of gene transfer. Mol. evol. biol. 19: 2226-2238.

  18. We are testing these ideas in an environmental gradient in the water holes of Cuatrocienegas. Coahuila,

  19. So.... the question is to know which is the type of species we are working with: a sexual, asexual or a “in-between species” in Bacteria is not so easy to sort out...

  20. A key to sort out which kind of bacteria we have is to learn which is the unit of selection ...

  21. III.-Which is the unit of selection?

  22. Amanda Castillo, Luis Eguiarte and Valeria Souza, ms. A case study in a “clonal” Pathogenic island (LEE) within a “clonal” species (E. coli). if the clonal model is true the unit of selection should the whole cassette LEE

  23. If the unit of selection is smaller than the island: the mosaic observed in the chromosome will repeat itself in the island like a Russian doll.

  24. LEE

  25. The Locus of Entero Effacement is responsible of the symptoms in EPEC, VTEC and EHEC clinical isolates Secretion system Type III LEE Secretion system Type III Secreted Proteins E.coli Tir Intimine Secreted Proteins Esp

  26. Molecular evolution analysis of 6 complete sequences of epidemic LEE Escherichia coli EPEC strain E2348/69 Escherichia coli EHEC O157:H7 EDL933 and Sakai O157 Escherichia coli EPEC RDEC-1 Escherichia coli STEC (LEE2) Citrobacter rodentium

  27. 45.0 42.5 40.0 37.5 35.0 whole island average 32.5 30.0 1 2 5 3 4 Average GC content of the five LEE operons.

  28. orf18 1.8 tir 1.6 eae 1.4 secretion system III espB 1.2 1 0.8 sepZ 0.6 0.4 0.2 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 Synonymous and non synonymous substitution rates for the 41 orfs of the LEE locus.

  29. strong purifying selection neutral line 1.2 1 0.8 0.6 0.4 0.2 0 eae TIR espD escR escU cesD escC escJ escN escD espA espB escS sepZ escV escT escF sepQ ORF2 ORF3 ORF4 ORF5 rORF1 rORF3 rORF6 rORF8 ORF10 ORF11 ORF12 ORF15 ORF16 ORF18 ORF19 ORF27 ORF29 rORF10 ORF1/Ler ORFU/cesT ORF30/espF rORF2/espG ORF23/sepL LEE genes dN/dS rate distribution of LEE locus genes.

  30. The LEE locus is not an homogeneous unit: Mutation + selection are acting with different intensity generating a mosaic. This is posible because recombination breaks the linkage. This is generated at the intimate regions of genes and its proteins.

  31. Which is the unit of selection if it is our intention to study adaptive molecular evolution? species population individual genome operons gene protein module nucleotide site The russian doll model

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