Download Bacterial species

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?
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 Mayr
1928
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
Silva
et al.
2003
Sympatric species in Rhizobium/ cohesive gene flow
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 outcompetes 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...).
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.
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?
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
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
The Locus of Entero Effacement is
responsible of the symptoms in
EPEC, VTEC and EHEC clinical
Secretion system
Type III
isolates
LEE
Secretion system
Type III
Secreted Proteins
E.coli
Tir
Intimine
Secreted Proteins
Esp
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
45.0
42.5
40.0
37.5
35.0
whole island average
32.5
30.0
1
2
3
4
5
Average GC content of the five LEE operons.
orf18
1.8
tir
1.6
eae
1.4
secretion system III
1.2
espB
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.
strong purifying selection
neutral line
1.2
1
0.8
0.6
0.4
0.2
0
LEE genes
dN/dS rate distribution of LEE locus genes.
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.
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