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 a theory-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 Sympatric species in Rhizobium/ cohesive gene flow Silva et al. 2003

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. ecotypes within a geographic region Species gene pool 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. 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 Amanda Castillo, Luis Eguiarte and Valeria Souza, ms.

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

26. 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 Molecular evolution analysis of 6 complete sequences of epidemic LEE

27. 12 34 5 Average GC content of the five LEE operons. whole island average 30.0 32.5 35.0 37.5 40.0 42.5 45.0

28. 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 1234567891011121314151617181920212223242526272829303132333435363738394041 Synonymous and non synonymous substitution rates for the 41 orfs of the LEE locus. orf18 secretion system III sepZ tir eae espB

29. 0 1.2 rORF1 rORF2/espG ORF1/Ler ORF2ORF3ORF4ORF5 escR escS escT escU rORF3 ORF10ORF11 cesDescC rORF6 escJ rORF8 sepZ ORF12 escV escN ORF15ORF16 sepQ ORF18 rORF10 ORF19 TIR ORFU/cesT eae escD ORF23/sepL espA espD espB ORF27 escF ORF29 ORF30/espF LEE genes dN/dS rate distribution of LEE locus genes. 0.2 0.4 0.6 0.8 1 neutral line strong purifying selection

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