Species

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 Mayrs 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 Phylogenet
ic 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.
5645787
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 O157H7 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
TIR
eae
escR
escS
escT
escU
cesD
escC
escJ
sepZ
escV
escN
sepQ
escD
espA
espD
espB
escF
ORF2
ORF3
ORF4
ORF5
rORF1
rORF3
ORF10
ORF11
rORF6
rORF8
ORF12
ORF15
ORF16
ORF18
ORF19
ORF27
ORF29
rORF10
ORF1/Ler
ORFU/cesT
rORF2/espG
ORF23/sepL
ORF30/espF
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