Species Populations Genotypes Valeria Souza & Luis Eguiarte HGT.

Species

Populations

GenotypesValeria 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?

I.- Do

species exist in bacteria, and what are their boundaries?

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 Mayr1928

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...

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.

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.

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),

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.

Chromosome Plasmids

Sympatric species in Rhizobium/ cohesive gene flow

Silva et al. 2003

II.- Which are the microevolutionary processes that lead to speciation in Bacteria?

or, How do bacteria break loose of the cohesion within the species?

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.).

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.

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

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...)

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...).

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.

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

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...

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

III.-Which is the unit of selection?

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.

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.

LEE

E.coli

LEE

Secretion systemType III

Secreted ProteinsEsp

Secretion systemType III

Secreted Proteins

TirIntimine

The Locus of Entero Effacement is responsible of the symptoms in EPEC, VTEC and EHEC clinical

isolates

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

1 2 3 4 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

0

0.2

0.4

0.6

0.8

1

1.2

1.4

1.6

1.8

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 ratesfor the 41 orfs of the LEE locus.

orf18

secretion system III

sepZ

tir eae

espB

0

1.2

rORF1

rORF2/espG

ORF1/Ler

ORF2

ORF3

ORF4

ORF5escRescSescTescU

rORF3

ORF10

ORF11cesDescC

rORF6escJ

rORF8sepZ

ORF12escVescN

ORF15

ORF16sepQ

ORF18

rORF10

ORF19TIR

ORFU/cesT ea

eescD

ORF23/sepLespAespDespB

ORF27escF

ORF29

ORF30/espF

LEE genes

dN/dS rate distribution of LEE locus genes.

0.2

0.4

0.6

0.8

1

neutral linestrong purifying selection

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.

speciespopulationindividual genomeoperonsgeneprotein modulenucleotide site

Which is the unit of selection if it is our intention to study adaptive molecular evolution?

The russian doll model