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17 Holmstrom, A. et al. (2001) LcrV is a channel size-determining
component of the Yop effector translocon of Yersinia. Mol. Microbiol.
39, 620–632
18 Sarker, M.R. et al. (1998) The Yersinia Yop virulon: LcrV is required
for extrusion of the translocators YopB and YopD. J. Bacteriol. 180,
1207–1214
19 Lee, V.T. et al. (2000) LcrV, a substrate for Yersinia enterocolitica type
III secretion, is required for toxin targeting into the cytosol of HeLa
cells. J. Biol. Chem. 275, 36869–36875
20 Derewenda, U. et al. (2004) The structure of Yersinia pestis V-antigen,
an essential virulence factor and mediator of immunity against
plague. Structure 12, 301–306
21 Mota, L.J. et al. (2005) Bacterial injectisomes: needle length does
matter. Science 307, 1278
22 Torruellas, J. et al. (2005) The Yersinia pestis type III secretion needle
plays a role in the regulation of Yop secretion. Mol. Microbiol. 57,
1719–1733
Vol.14 No.5 May 2006
23 Journet, L. et al. (2003) The needle length of bacterial injectisomes is
determined by a molecular ruler. Science 302, 1757–1760
24 Brubaker, R.R. (2003) Interleukin-10 and inhibition of innate
immunity to Yersiniae: roles of Yops and LcrV (V antigen). Infect.
Immun. 71, 3673–3681
25 Nilles, M.L. et al. (1997) Yersinia pestis LcrV forms a stable complex
with LcrG and may have a secretion-related regulatory role in the lowCa2C response. J. Bacteriol. 179, 1307–1316
26 Sing, A. et al. (2005) A hypervariable N-terminal region of
Yersinia LcrV determines Toll-like receptor 2-mediated IL-10 induction and mouse virulence. Proc. Natl. Acad. Sci. U. S. A. 102,
16049–16054
0966-842X/$ - see front matter Q 2006 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tim.2006.02.010
Genome Analysis
The Neolithic revolution of bacterial genomes
Alex Mira, Ravindra Pushker and Francisco Rodrı́guez-Valera
Evolutionary Genomics Group, Division of Microbiology, Universidad Miguel Hernandez, San Juan 03550, Alicante, Spain
Current human activities undoubtedly impact natural
ecosystems. However, the influence of Homo sapiens on
living organisms must have also occurred in the past.
Certain genomic characteristics of prokaryotes can be
used to study the impact of ancient human activities on
microorganisms. By analyzing DNA sequence similarity
features of transposable elements, dramatic genomic
changes have been identified in bacteria that are
associated with large and stable human communities,
agriculture and animal domestication: three features
unequivocally linked to the Neolithic revolution. It is
hypothesized that bacteria specialized in human-associated niches underwent an intense transformation after
the social and demographic changes that took place
with the first Neolithic settlements. These genomic
changes are absent in related species that are not
specialized in humans.
The Neolithic revolution
Before the Neolithic period, human survival was linked to
the hunter-gatherer culture and populations were small
and scattered [1]. Approximately 10 000 years ago,
however, the advent of agriculture and animal husbandry
brought the largest social revolution in the history of
humankind [2]. Food resources were more abundant and
constant, and the human species increased its population
size at an extraordinary annual growth rate of 0.1% [3].
From the point of view of bacterial pathogens, humans
suddenly became attractive hosts; they concentrated large
populations on limited areas, which maximized the chance
for transmission between longer-lived carriers. Thus, it is
Corresponding author: Mira, A. ([email protected]).
Available online 29 March 2006
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likely that human population growth and expansion
during the Neolithic created a selective pressure that
favoured pathogens that specialized in human hosts,
originating what was probably the first wave of emerging
human diseases [4].
One of the features that has emerged from fully
sequenced genomes is that species that have specialized
their niche undergo a process of reductive evolution
through gene elimination [5–8]. Mobile elements such as
insertion sequences (ISs) greatly increase in number
following host restriction [9] and influence the process of
genome reduction. After a niche change, many genes
become obsolete and the selective pressure to preserve
their function is dramatically reduced. In addition, host
restriction can reduce the efficiency of selection in
bacterial specialists because of reduced population sizes
and genetic drift [10,11]. ISs might inactivate unnecessary
or redundant genes in the new environment [12,13] by
rapidly increasing the number of IS copies. The number of
IS elements in bacterial pathogens could, therefore,
indicate a recent host adaptation [14] or restriction [9].
Here, we show that recent expansions of ISs in bacteria
are associated with humans or human activities that were
developed in the Neolithic. The cultural revolution of the
Neolithic can be dated precisely (for evolutionary time
scales) at w10 000 years before present, which provides
an outstanding model for prokaryotic evolution in the
short-to-medium time scale.
Recent expansions of mobile elements
We investigated paralogous genes, including IS elements,
across 255 fully sequenced prokaryotic genomes. Paralogues are defined as protein-coding sequences within a
genome that have at least 30% sequence identity over
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(a)
100
90
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0.5
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1.5 2.0 2.5 3.0
Gene position (Mbp)
(b)
3.5
100
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0
4.0
1
2
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4
Gene position (Mbp)
Shigella flexneri 2a str. 301
100
90
80
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60
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30
0
0.5 1.0 1.5
2.0 2.5
3.0 3.5 4.0
4.5
Gene position (Mbp)
5
Escherichia coli K12
Sequence identity (%)
Sequence identity (%)
Bordetella bronchiseptica RB50
Sequence identity (%)
Sequence identity (%)
Bordetella pertussis Tohama I
100
90
80
70
60
50
40
30
0
0.5 1.0 1.5
2.0 2.5
3.0 3.5 4.0 4.5
Gene position (Mbp)
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Figure 1. IS expansions in human-related species. DNA sequence similarity between pairs of paralogous genes (blue crosses) and between pairs of IS elements (red crosses)
is indicated across different bacterial species. Chromosomal location of the first gene for each pair is shown on the x-axis. (a) Bordetella pertussis Tohama I and Bordetella
bronchiseptica RB50; (b) Shigella flexneri 2a and Escherichia coli K12. Bacteria specialized in humans are shown on the left, whereas related species that are not human
specialists are shown on the right. Species associated with humans (B. pertussis and S. flexneri) show a recent explosion of IS elements across their genomes.
O60% of their lengths [15–17]. To estimate DNA sequence
similarity, global alignments were performed on the gene
pairs using Stretcher [18]. When a frequency histogram of
paralogue sequence similarity was plotted, we observed
that most paralogues across taxa display 40–60% DNA
sequence similarity, followed by a second group of
duplicated genes at 90–100% similarity. This second
group presumably contains recently formed paralogues
and a few genes with a high protein-dosage requirement,
the DNA sequence of which is kept identical by gene
conversion mechanisms [19]. However, a closer look
reveals that most of the members in this group are ISs
or IS-transposase genes. Interestingly, 69 out of 89
bacteria in which O75% of the recently formed paralogous
genes correspond to ISs are species that are uniquely
associated with humans (Figure 1). Most of the other cases
correspond to host-associated species such as invertebrate
symbionts or pathogens. These include the mutualist
Photorhabdus luminescens, which is specifically associated with nematodes, and the reproductive parasite of
insects Wolbachia pipientis (Figure 2a). This indicates
that any niche specialization normally involves IS
expansions [9]. A few cases of free-living species with
recent IS expansions are also observed, such as
the sediment-isolated species Shewanella oneidensis or
Geobacter metallireducens (Figure 2b). Examples
of pathogens specialized in humans (Figure 1)
include Bordetella pertussis, a species that has recently
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undergone an extraordinary paralogue expansion only as
a result of ISs (Figure 1a); however, Bordetella bronchiseptica, a species that can infect different hosts and live
freely in the environment, has a normal distribution of
DNA similarity across paralogues. The IS expansion not
only inactivates genes by insertion but also increases the
rate of genome rearrangements [11]. The human pathogen
Shigella flexneri, which is closely related to the saprophytic Escherichia coli K12 strain, has recently undergone
another IS expansion (Figure 1b). We hypothesize that
mobile element expansion took place in Neolithic times
when ancestors of these two species independently
restricted their host range to humans. Three lines of
evidence support the hypothesis that the expansion
occurred at that moment. First, IS expansions are also
observed in bacteria associated with domestication
processes typical of the Neolithic transition. Second, the
substitution rate between IS elements is virtually zero,
which is consistent with a single, recent event. And third,
divergence estimates between IS-loaded human specialists and IS-free generalists are consistent with the
Neolithic hypothesis.
Pathogens of domesticated plants and livestock
Pathogens of agricultural plants and domesticated
animals also seem to have undergone recent episodes of
IS expansion. Thus, the genomes burdened with ISs are
those related to the three main changes that are
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(a)
Photorhabdus luminescens laumondii TTO1
Wolbachia pipientis wMel
100
Sequence identity (%)
Sequence identity (%)
100
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1.0
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0
1
2
Geobacter metallireducens GS-15
5
6
Shewanella oneidensis MR-1
Sequence identity (%)
100
Sequence identity (%)
4
Gene position (Mbp)
Gene position (Mbp)
(b)
3
90
80
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0.5
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Gene position (Mbp)
0
0.5
1.0
1.5
2.0
2.5
3.0
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5.0
Gene position (Mbp)
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Figure 2. IS expansions in species that are presumably unrelated to humans. DNA sequence similarity is indicated between pairs of paralogous genes (blue crosses) and
between pairs of IS elements (red crosses). (a) Wolbachia pipientis (which causes cytoplasmic incompatibility in the fruit fly Drosophila melanogaster) and Photorhabdus
luminescens (a mutualistic symbiont with a restricted host range to the nematode Heterorhabditis bacteriophora) are animal-associated. (b) Geobacter metallireducens and
Shewanella oneidensis are metal reducers from the terrestrial subsurface.
unequivocally linked to the Neolithic transition: agriculture, animal domestication and the formation of larger
human communities. For example, several sequenced
species of Pseudomonas are versatile microorganisms
that live in soil or water. However, Pseudomonas syringae
DC3000 (a pathovar that is specialized for tomato plants
[20]) has undergone a massive episode of IS expansion,
with most mobile elements sharing O98% sequence
similarity (Figure 3a). Because crops are abundant and
concentrated on certain regions, they are likely to
represent an attractive niche for plant pathogens. Such
pathogens include different species of Xanthomonas such
as Xanthomonas axonopodis pv. citri, which is specialized
in citrus trees and contains an extraordinary number of IS
elements [21]. The rice pathogen Xanthomonas oryzae is
even more extreme and contains O800 ISs [22], and
although the sequences of related species that are not
plant specialists are unavailable for comparison, the
reason behind this genomic change is likely to be related
to the specialization of Xanthomonas in rice plants after
the expansion of this staple food across Asia.
The genomes of bacteria specialized in farm animals
also seem to be affected. The species Burkholderia mallei
is an obligate parasite of horses, donkeys and mules, with
no other known natural reservoir [23]. Thus, it seems
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likely that it specialized in these animals after the wild
ancestors of horses were domesticated, which increased
their population size and lifespan. The expansion of IS
elements is also dramatic in this species (Figure 3b),
whereas its sister species – the soil inhabitant Burkholderia pseudomallei – contains a limited number of IS
elements [24]. Because the domestication of horses seems
to have occurred relatively recently in human history
(w4500 years ago [25]), the speed of these genomic
changes mediated by ISs must have been extraordinary.
Furthermore, bacteria associated with food production
also seem to have undergone transposase amplification at
a genomic scale. The domesticated lactic-acid bacterium
Lactococcus lactis [26] is the most commonly used cheese
starter in the world. This species has been used for
generations to inoculate cheese, which has effectively
maintained a domestic culture of the bacterium that is
associated with human populations. When compared with
sequenced related species, L. lactis shows a distinctive
recent expansion of IS elements (Figure 3c). We predict
that other bacterial species that are associated with
traditional human food (such as those involved in yoghurt
or wine production and the preservation of foods in brine
or salt) might have undergone similar mobile-element
expansions (e.g. Ref. [27]).
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Vol.14 No.5 May 2006
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(a)
Pseudomonas syringae tomato
Pseudomonas aeruginosa PA01
100
Sequence identity (%)
Sequence identity (%)
100
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3
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Gene position (Mbp)
(b)
Burkholderia mallei ATCC 23344
Burkholderia pseudomallei K96243
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Sequence identity (%)
Sequence identity (%)
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Gene position (Mbp)
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(c)
Lactococcus lactis subsp. lactis
Lactobacillus acidophilus NCFM
100
Sequence identity (%)
Sequence identity (%)
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Figure 3. IS expansions in bacteria that are specialized in agricultural plants, in farm animals and in food processing. DNA sequence similarity is indicated between pairs of
paralogous genes (blue crosses) and between pairs of IS elements (red crosses) across different bacterial species. (a) Pseudomonas syringae pv. tomato and Pseudomonas
aeruginosa PA01; (b) Burkholderia mallei ATCC 23344 and Burkholderia pseudomallei K96243; (c) Lactococcus lactis subsp. lactis and Lactobacillus acidophilus NCFM.
Specialized strains are shown on the left and non-specialized related strains are shown on the right.
Predicting niche specialization
As more information accumulates about species that have
experienced genomic changes linked to ISs, it can be used
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in the reverse direction: recent lifestyle changes in bacteria
could be predicted and ISs might even provide an
approximate time scale for these genomic events. For
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Bradyrhizobium japonicum USDA 110
(a)
100
Mesorhizobium loti MAFF303099
Sequence identity (%)
Sequence identity (%)
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90
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Halobacterium salinarum NRC-1
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Haloarcula marismortui ATCC 43049
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Sequence identity (%)
Sequence identity (%)
100
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TRENDS in Microbiology
Figure 4. IS expansions in species under potential human influence. DNA sequence similarity is indicated between pairs of paralogous genes (blue crosses) and between
pairs of IS elements (red crosses) across selected bacterial species. Chromosomal location of the first gene for each pair is shown on the x-axis. (a) Bradyrhizobium japonicum
USDA 110 and Mesorhizobium loti MAFF303099; (b) Halobacterium salinarum NRC-1 and Haloarcula marismortui ATCC 43049. Species on the left show recent IS element
expansions that are not found in closely related species (right), which is hypothesized to be the result of niche specialization.
example, the genome of the legume symbiont Bradyrhizobium japonicum displays a large expansion of nearly
identical transposases whereas another nodule-forming
symbiont, Mesorhizobium loti, contains older transposases
(Figure 4a). If our hypothesis is correct, the reason for this
could be related to the formation of B. japonicum nodules in
the widely cultivated soya bean. By contrast, M. loti has not
been domesticated, is associated with several wild plants
and has a wider host range [28]. The genome of the
halophilic archaeon Halobacterium salinarum shows a
recent IS expansion when compared with related species
(Figure 4b). Although it could be claimed that this species is
not related to humans, a closer look at its niche reveals that
H. salinarum was isolated from salted fish. The extraction
of salt is one of the oldest human activities for preserving
food and was used by the ancient Chinese as long ago as
9000 BC [29]. As environments characterized by high salt
concentrations expanded, a new human-associated niche
extended across the globe and prokaryotes could have
adapted to it. Similarly, genomic features such as IS
expansions in other genomes could serve as hints of
ecological changes*.
The opposite scenario is also interesting. There might
be cases of bacteria that are clearly specialized in humans
but have no traces of IS expansion. Mycobacterium leprae
(the causative agent of leprosy) could be one of the few
* Plots for all studied species are available from the authors upon request.
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examples. It contains no ISs even though they could have
expanded across the two-thirds of the genome that are no
longer necessary in its specialized niche [6]. Instead, the
genome of M. leprae has undergone an incomplete
reductive evolution process and has retained 1000
pseudogenes with a near-normal length. Perhaps the
intracellular lifestyle has precluded it from incorporating
ISs and the extraordinary number of pseudogenes is
because of the absence of transposases, which has slowed
down the pace of genome reduction. IS elements, when
present, quickly inactivate genes [13] and regulatory
elements [30], and serve as repetitive sequences that
induce large deletions [31]. Thus, the expansion of ISs
might function as a mechanism for facilitating
ecological adaptation.
Dating the IS expansion
Dating divergence in bacterial lineages is a difficult task
as a result of (among other things) the absence of a fossil
record, the difficulty of calibrating a molecular clock and
the meagre knowledge about generation times in nature
[32,33]. The ribosomal 16S rRNA gene is estimated to
diverge at a rate of w1–2% per 50 million years [32–35],
using geological events that could be dated between 50
million and 500 million years. Although this gene seems to
be too conserved to date relatively recent events, it is
interesting to note that the observed divergences are
similar among the different pairs studied here:
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Vol.14 No.5 May 2006
205
Table 1. Sequence divergence in IS-interrupted ORFs and in fully sequenced genomes of putative Neolithic speciesa
(a) Divergence between IS-interrupted ORFs and functional homologues in related strains
Species with
IS-interrupted
ORFs
Yersinia pestis
CO92
Yersinia pestis
CO92
Shigella
flexneri 2a
Burkholderia
mallei
Bordetella
pertussis
Shigella
flexneri 301
Shigella
flexneri 301
Pseudomonas
syringae
tomato
Fc
Average
similarityd
He
Average
similarityf
Average genomic
dSg
Divergence
estimateh
Refs
26
23
99.992
3442
99.872
0.00008G0.00002
6000 years
[37,38]
Yersinia
pseudotuberculosis
Escherichia coli K12
26
24
99.756
3413
99.154
0.00217G0.0002
11 000 years
[37,38]
77
56
97.399
3195
98.403
0.0436G0.00076
N/A
N/A
Burkholderia
pseudomallei
Bordetella
parapertussis
Shigella
flexneri 2457T
Shigella sonnei
43
41
99.584
2535
99.214
0.01647G0.00036
N/A
N/A
122
60
98.914
2880
98.713
0.0451G0.00124
N/A
N/A
77
58
99.693
3449
99.859
0.00047G0.00006
N/A
N/A
77
64
98.185
3034
98.361
0.03693G0.0008
N/A
N/A
43
21
86.549
3988
93.81
0.6279G0.0104
N/A
N/A
Species with
functional
homologue
Yersinia pestis KIM
Pseudomonas
syringae
phaseolicola
Nb
(b) Synonymous divergence between fully sequenced genomes of
putative Neolithic species and related strains
a
Abbreviation: N/A, not applicable.
Number of genes interrupted by ISs.
c
Number of IS-interrupted ORFs with a functional homologue in a related strain.
d
Average DNA similarity between the IS-interrupted ORFs and functional homologues.
e
Number of homologous genes identified by reciprocal best-hit method.
f
Average DNA similarity of all homologues between the two genomes.
g
dS, synonymous substitution rate per synonymous site, estimated by maximum likelihood [42].
h
Estimates in Y. pestis are included for reference.
b
divergences in the 16S rRNA genes were 0.15% between
Bu. mallei and Bu. pseudomallei, and 0.2% for the E. coli
K12–S. flexneri pair and the Bo. pertussis–Bo. parapertussis pair. A larger divergence of 0.9% was observed for
the P. syringae pathovars P. syringae syringae and P.
syringae tomato. A 0.24% divergence was observed for the
two sequenced strains of S. flexneri.
A more direct estimate of IS expansions comes from
studying the genes that have been inactivated by IS
insertion. Under the assumption that these truncated
genes lost functionality at the time of the insertion, the
date of the IS expansion can be estimated by investigating
the divergence of truncated open reading frames (ORFs).
Being pseudogenes, all mutations can be considered to be
selectively neutral [36]. We identified ORFs that are
putative pseudogenes as a result of the insertion of ISs
[13] and selected those for which a functional homologue
could be found in related strains or species (Table 1a). The
estimated divergence was then compared with that of the
IS-interrupted genes in Yersinia pestis, one of the few
species in which the age of diversification has been firmly
calculated [37,38]. To extrapolate these estimations to
other bacteria is necessarily a crude approximation
because it assumes similar molecular substitution rates.
Nevertheless, the levels of nucleotide divergence for the
IS-generated pseudogenes are reasonably close to the
Neolithic time frame, except for the pseudomonads.
A similar result is obtained when divergence rates are
investigated at synonymous sites in homologous genes in
the species studied (Table 1b). Using complete sequenced
genomes, we have calculated synonymous substitution
rates (dS) for whole genome pairs. Again using the
estimated divergence time for Y. pestis as a reference,
the genomes of Shigella, Bordetella and Burkholderia
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species seem to have expanded within a range of
thousands of years in the past. Burkholderia showed
more recent divergence estimates than the rest, which is
consistent with the later domestication of horses. Outside
the prokaryotes, it is interesting to note that the malaria
parasite and human specialist Plasmodium falciparum
also shows low levels of variation and is estimated to have
originated as a clone w6000 years ago [39].
Although approximate, these estimates place the
explosion of IS elements within the historical range rather
than within longer, geological timescales. The speed
reported here at which ISs can expand is supported by
laboratory experiments in which IS elements were
detected to replicate and insert across the genome as
early as after 500 generations [40]. Specializing in a given
environment such as the human host or human-related
plants or animals probably rendered many genes
unnecessary and widened the possible sites for non-lethal
insertions. Therefore, bacteria could have undergone the
Neolithic revolution as much as humans did, and the
genomes of those bacteria still carry the tell-tale prints in
the form of extended IS element families.
Conclusions and future perspectives
The work presented here shows that expansions of
transposable elements in bacterial genomes can be
reliable indicators of specialization to human-related
niches. We anticipate that parallel genomic changes
could be taking place in other human-related organisms
such as domesticated fungal species involved in traditional food production or eukaryotic unicellular parasites. The remarkable speed at which bacteria have
adapted to human cultural evolution underscores the
evolutionary plasticity of the prokaryotic cell, which can
206
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TRENDS in Microbiology
probably be matched only by viral evolution [41]. The
central role of IS elements described here and the use of
their sequence divergence to identify recent niche
specialization events could prove a useful approach to
detect other (not necessarily human-related) recent
environmental specializations. Furthermore, we propose
that analysis of the type of genes inactivated in the IS
insertion process might give hints as to the nature of the
environmental change. Although the pseudogenes generated by IS elements are quickly eroded by deletional bias
[8], their function could give useful information in recent
specialization processes. In addition, older events would
leave a trace of divergent ISs. The relatively new science of
comparative genomics might provide a powerful tool to
understand better the ecology and evolution of prokaryotes. This will be better elucidated when more genome
sequences are available from non-human pathogens.
Acknowledgements
A.M. is a recipient of a ‘Ramón y Cajal’ research contract from the Spanish
Ministry of Science and Education. Support from I.S. Carlos III (04/1319)
and the EU project GEMINI (QLK3-CT-2002-02056) is also acknowledged. We thank S.B. Ingham for help with the figures and G. Nyiro and F.
Kunst for providing information about host specificity in Wolbachia and
Photorhabdus species.
References
1 Childe, V.G. (1925) The Dawn of European Civilization, 5th edn,
Routledge & Kegan Paul
2 Bocquet-Appel, J.P. (2002) Paleoanthropological traces of Neolithic
demographic transition. Curr. Anthropol. 43, 637–650
3 Eshed, V. et al. (2004) Has the transition to agriculture reshaped the
demographic structure of prehistoric populations? New evidence from
the Levant. Am. J. Phys. Anthropol. 124, 315–329
4 McKeown, T. (1988) The Origins of Human Disease, 1st edn, Blackwell
5 Andersson, J.O. and Andersson, S.G. (1999) Insights into the
evolutionary process of genome degradation. Curr. Opin. Genet. Dev.
9, 664–671
6 Cole, S.T. et al. (2001) Massive gene decay in the leprosy bacillus.
Nature 409, 1007–1011
7 Moran, N.A. and Mira, A. (2001) The process of genome shrinkage in
the obligate symbiont Buchnera aphidicola. Genome Biol. 2,
research0054
8 Mira, A. et al. (2001) Deletional bias and the evolution of bacterial
genomes. Trends Genet. 17, 589–596
9 Moran, N.A. and Plague, G.R. (2004) Genomic changes following host
restriction in bacteria. Curr. Opin. Genet. Dev. 14, 627–633
10 Moran, N.A. (1996) Accelerated evolution and Muller’s rachet in
endosymbiotic bacteria. Proc. Natl. Acad. Sci. U. S. A. 93, 2873–2878
11 Parkhill, J. et al. (2003) Comparative analysis of the genome
sequences of Bordetella pertussis, Bordetella parapertussis and
Bordetella bronchiseptica. Nat. Genet. 35, 32–40
12 Wei, J. et al. (2003) Complete genome sequence and comparative
genomics of Shigella flexneri serotype 2a strain 2457T. Infect. Immun.
71, 2775–2786
13 Lerat, E. and Ochman, H. (2004) J-F: exploring the outer limits of
bacterial pseudogenes. Genome Res. 14, 2273–2278
14 Parkhill, J. et al. (2001) Genome sequence of Yersinia pestis, the
causative agent of plague. Nature 413, 523–527
15 Altschul, S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new
generation of protein database search programs. Nucleic Acids Res.
25, 3389–3402
16 Pushker, R. et al. (2004) Comparative genomics of gene-family size in
closely related bacteria. Genome Biol. 5, R27
17 Brown, S.M. (2000) Bioinformatics: A Biologist’s Guide to Biocomputing and the Internet (1st edn), pp. 57–84, Eaton Publishing
www.sciencedirect.com
Vol.14 No.5 May 2006
18 Rice, P. et al. (2000) EMBOSS: the European Molecular Biology Open
Software Suite. Trends Genet. 16, 276–277
19 Abdulkarim, F. and Hughes, D. (1996) Homologous recombination
between the tuf genes of Salmonella typhimurium. J. Mol. Biol. 260,
506–522
20 Buell, C.R. et al. (2003) The complete genome sequence of the
Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato
DC3000. Proc. Natl. Acad. Sci. U. S. A. 100, 10181–10186
21 da Silva, A.C. et al. (2002) Comparison of the genomes of two
Xanthomonas pathogens with differing host specificities. Nature 417,
459–463
22 Lee, B.M. et al. (2005) The genome sequence of Xanthomonas oryzae
pathovar oryzae KACC10331, the bacterial blight pathogen of rice.
Nucleic Acids Res. 33, 577–586
23 Alibasoglu, M. et al. (1986) Glanders outbreak in lions in the Istanbul
zoological garden. Berl. Munch. Tierarztl. Wochenschr. 99, 57–63
24 Nierman, W.C. et al. (2004) Structural flexibility in the Burkholderia
mallei genome. Proc. Natl. Acad. Sci. U. S. A. 101, 14246–14251
25 Jansen, T. et al. (2002) Mitochondrial DNA and the origins of the
domestic horse. Proc. Natl. Acad. Sci. U. S. A. 99, 10905–10910
26 Bolotin, A. et al. (2001) The complete genome sequence of the lactic
acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res. 11,
731–753
27 Prust, C. et al. (2005) Complete genome sequence of the acetic
acid bacterium Gluconobacter oxydans. Nat. Biotechnol. 23,
195–200
28 Jordan, D.C. (1984) Family Rhizobiaceae. In Bergey’s Manual of
Systematic Bacteriology (Vol. 1, 1st edn) (Krieg, N.R. and Holt, J.G.,
eds), pp. 234–244, Williams & Wilkins
29 Kurlansky, M. (2002) Salt: A World History, 1st edn, Vintage Canada
30 Mira, A. and Pushker, R. (2005) The silencing of pseudogenes. Mol.
Biol. Evol. 22, 2135–2138
31 Schneider, D. et al. (2000) Long-term experimental evolution in
Escherichia coli. IX. Characterization of insertion sequence-mediated
mutations and rearrangements. Genetics 156, 477–488
32 Ochman, H. and Wilson, A.C. (1987) Evolution in bacteria: evidence
for a universal substitution rate in cellular genomes. J. Mol. Evol. 26,
74–86
33 Ochman, H. et al. (1999) Calibrating bacterial evolution. Proc. Natl.
Acad. Sci. U. S. A. 96, 12638–12643
34 Clark, M.A. et al. (1999) Sequence evolution in bacterial endosymbionts having extreme base compositions. Mol. Biol. Evol. 16,
1586–1598
35 Wernegreen, J.J. and Moran, N.A. (1999) Evidence for genetic drift in
endosymbionts (Buchnera): analyses of protein-coding genes. Mol.
Biol. Evol. 16, 83–97
36 Gojobori, T. et al. (1982) Patterns of nucleotide substitution in
pseudogenes and functional genes. J. Mol. Evol. 18, 360–369
37 Achtman, M. et al. (1999) Yersinia pestis, the cause of plague, is a
recently emerged clone of Yersinia pseudotuberculosis. Proc. Natl.
Acad. Sci. U. S. A. 96, 14043–14048
38 Achtman, M. et al. (2004) Microevolution and history of the plague
bacillus, Yersinia pestis. Proc. Natl. Acad. Sci. U. S. A. 101,
17837–17842
39 Rich, S.M. et al. (1998) Malaria’s Eve: evidence of a recent population
bottleneck throughout the world populations of Plasmodium falciparum. Proc. Natl. Acad. Sci. U. S. A. 95, 4425–4430
40 Schneider, D. and Lenski, R.E. (2004) Dynamics of insertion sequence
elements during experimental evolution of bacteria. Res. Microbiol.
155, 319–327
41 Zanotto, P.M. et al. (1996) Population dynamics of flaviviruses
revealed by molecular phylogenies. Proc. Natl. Acad. Sci. U. S. A.
93, 548–553
42 Yang, Z. (1997) PAML: a program package for phylogenetic analysis by
maximum likelihood. Comput. Appl. Biosci. 13, 555–556
0966-842X/$ - see front matter Q 2006 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tim.2006.03.001