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© 2006 Nature Publishing Group
Genetic mechanisms and evolutionary
significance of natural variation
in Arabidopsis
Thomas Mitchell-Olds
1
& Johanna Schmitt
2
Genomic studies of natural variation in model organisms provid e a bridge between molecular analyses of gene function
and evolutionary investigations of adaptation and natural selection. In the model plant species Arabidopsis thaliana,
recent studies of natural variation have led to the identification of genes underlying ecologically important complex
traits, and provided new insights about the processes of genome evolution, geographic popula tion structure, and the
selective mechan isms shaping complex trait variation in natural populations. These advances illustrate the potential for
a new synthesis to elucidate mechanisms for the adaptive evolution of complex traits from nucleotide sequences to
real-world environments.
T
he beginning of the twenty-first century is an exciting time for
biologists. Rapid advances in genomics have changed our
view of the biological world and fostered new links between
molecular biology, ecology and evolution. Genomic studies of
natural variation in model organisms are a crucial ingredient in this
new synthesis. Molecular biologists have begun to exploit natural
variation to identify the genetic mechanisms underlying complex
traits
1
. Simultaneously, these new genomic tools make it possible for
evolutionary biologists to study how ecologically important complex
traits evolve in natural environments. These advances now make it
possible to understand the adaptive evolution of complex trait
variation from molecular mechanisms to geographic patterns of
population structure and natural selection.
The diminutive weed Arabidopsis thaliana provides an ideal system
for such interdisciplinary synthesis. This species
—
a close relative of
Brassica crops such as mustard and broccoli
—
is a convenient genetic
model because of its short generation time and small genome. The
A. thaliana genome was the first plant genome to be sequenced, and
the ge nes and developmental pathways controlling ecologically
important traits such as germination, flowering time, pest resistance,
and stress tolerance are rapidly being elucidated. It is therefore
possible to identify ‘candidate’ genes for adaptive variation in natural
populations. A. thaliana is a widespread annual weed of rocky places
and disturbed sites, native to Europe and central Asia and naturalized
in North America (Fig. 1). Across this geographic range, it experi-
ences a broad range of climatic conditions
2
and selective pressures.
Inbred stocks are available for many natural A. thaliana accessions
(‘ecotypes’), originating across the species’ range. Because the species
is habitually inbreeding, genomic and phenotypic data can be
combined from multiple exper iments with the same genotypes.
These genomic tools and resources have enabled a number of
important advances in molecular and evolutionary genetics. Here
we focus on advances in three complementary areas: (1) genomic
studies of molecular variation and population structure; (2) identi-
fication of genetic polymorphisms underlying natural variation in
complex traits; and, (3) ecolog ica l and evolutionary studies of
natural selection and adaptation. Taken together, these advances
now make it possible to identify the genetic mechanisms underlying
the adaptive evolution of complex traits in natural populations.
Molecular variation and population structure
How much molecular polymorphism exists in A. thaliana? Recent
genome-wide studies show that an average pair of alleles differs at
about seven nucleotides per kilobase (kb; nucleotide diversity ¼ 0.007;
refs 3, 4). T his is about 50% lower than polymorphi sm in the
outcrossing congener A. lyrata ssp. petraea
5
, roughly the same as
Drosophila melanogaster
6
, and nearly an order of magnitude higher
than humans
7
. A. thaliana has a high frequency of self-pollination in
the wild
8
, hence individuals are homozygous at most loci
3
. Such high
rates of self-pollination may influence patterns of linkage disequi-
librium, which provides the basis for association studies and linkage
disequilibrium mapping in human genetics and plant breeding (see
Box 1).
Patterns of nucleotide polymorphism contain a signature of
historical demography and natural selection (see Box 2). Genome-
wide information for A. thaliana has enabled fundamental advances
in our understanding of the evolutionary processes that influence
these patterns. In many species, a positive correlation exists between
local recombination rates and levels of nucleotide diversity
3
.In
regions of low recombination, genetic variation may be reduced
owing to ‘hitchhiking’ of neutral variation with nearby selected sites,
which will influence w ider chromosomal regions when recombina-
tion is low. However, this reduction in variation could be due either
to selective sweeps of advantageous mutations, or to background
selection, which eliminates deleterious mutations and the haplotypes
that carry them. Genome-wide polymorphism data make it possible to
distinguish these possibilities. The recent observation
3
that nucleotide
polymorphism is negatively correlated with gene density supports
background selection as the predominant mechanism. Gene-dense
regions show little sign of rare variants attributable to recent selective
sweeps, but the frequencies of non-synonymous polymorphisms
indicate purifying selection against deleterious mutations
9
.
REVIEWS
1
Department of Biology, PO Box 91000, Duke University, Durham, North Carolina 27708, USA.
2
Department of Ecology and Evolutionary Biology, Box G-W, Brown University,
Providence, Rhode Island 02912, USA.
Vol 441|22 June 2006|doi:10.1038/nature04878
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© 2006 Nature Publishing Group
Nevertheless, surveys of A. thaliana ecotypes have identified loci
that may have undergone recent positive selection or selective sweeps
(Box 2)
10
. Certain other loci show unusually high levels of amino-
acid variation or too many intermediate-frequency nucleotide poly-
morphisms, which exceed neutral expectation and may have been
maintained by natural selection
11–13
. The selective mechanisms main-
taining such polymorphisms remain an important open question.
Allelic polymorphisms may be maintained within populations by
frequency-dependent selection (where common genotypes have low
fitness, and rare types are favoured), by temporal variation in
selection across seasons and years, or by epistatic selection in
which the fitness of an allele depends on genetic backg round
14
.
Alternatively, different alleles might be maintained in different
populations by local adaptation to geographically divergent selec-
tion, resulting in excess polymorphism species-wide, but little
variation within individual populations. Wide sur veys of A. thaliana
ecotypes cannot distinguish between these different ecological
mechanisms, because information is also needed about patterns of
variation within undisturbed natural populations. However, human
disturbance and admixture of different source pop ulations may
complicate such studies in most parts of the A. thaliana range. It is
therefore impor tant to understand the geographic population
structure of natural v ariation within the species, as well as the
distribution of molecular variation within and among populations
across the species range.
Genome-wide polymorphism data for ecotypes across the range of
A. thaliana have made it possible to investigate th e geographic
structure of molecular variation. The genetic divergence and geo-
graphic distance between pairs of populations is positively correlated
across the native range
3,15
. Such ‘isolation by distance’ reflects long-
term geographical isolation with limited gene flow. The pattern of
population ancestry of European ecotypes suggests that much of
the native range was colonized from several glacial refugia, with
admixture in the zones colonized from more than one source.
However, recent human disturbance tends to homogenize variation
among populations, especially in agricultural regions of Europe and
introduced populations in North America
15–17
.
How is molecular polymorphism distributed within and among
natural populations of A. thaliana? Recent studies have estimated the
proportion of total molecular polymorphism that is found within
populations to be near 45% in western Europe and North Amer-
ica
16–18
, but only 12% in less-disturbed parts of Norway
19
. Although
part of this difference may be attributable to loss of variability as
A. thaliana migrated north from circum-Mediterranean refugia,
comparisons across a 900-km north–south transect in Norway find
no latitudinal changes in genetic variation. Therefore, low variation
within Norwegian populations is probably not attributable to post-
Pleistocene founder events. Instead, high variability w ithin western
European populations probably reflects admixture resulting from
human disturbance
18
. Such admixture complicates our ability to
understand the evolutionary forces shaping genetic variation within
A. thaliana populations.
Finding the genes underlying trait variation
Natural selection operates on complex trait phenotypes. In order to
understand the evolution of ecologically important variation, we
Figure 1 | Arabidopsis habitats. a, b, Although commonly found in
disturbed sites, A. thaliana also grows in pine forests on sandy soils
(a; Bastan, western Siberia) and perennial grasslands in sites with sparse
vegetation (b; Stepnoje, western Siberia). c, Introduced populations in
North America may number in the millions. Here, the white flowers are
another species, but the interspersed vegetation is predominantly A. thaliana
(Michigan, USA). d, Even in western Europe it can be a long-term resident of
stone walls and other sites (Cologne, Germany). (Russia photographs by
M. Hoffmann; USA photograph by J. Bergelson; Ger many photograph by
A. Wilczek.)
Box 1 | Association studies
Association studies use linkage disequilibrium to identify
polymorphisms that may be responsible for complex trait variation.
Linkage disequilibrium quantifies statistical correlations between
polymorphic sites: when linkage disequilibrium is present then
information from one locus provides some predictive information
about the genotype at a second locus. Association studies take
advantage of recombinations accumulated over thousands of
generations, and hence may aid identification of individual genes
responsible for QTL. In the past (top panel), a new mutation
(triangle) occurs at a quantitative trait locus. The original population
contains an ancestral chromosome on which the new mutation
occurred (black line), as well as other chromosomes (grey lines).
After many generations of recombination, the present-day
population (lower panel) contains short chromosome regions
derived from the original population. Molecular markers near the
causal polymorphism (b) will be correlated with phenotype, whereas
distant markers (a, c) are uncorrelated because they have been
reshuffled by recombination. On average, in A. thaliana
polymorphisms separated by .50 kb are usually statistically
independent, whereas linkage disequilibrium is substantial between
sites separated by ,50 kb (ref. 71). Because these regions in
disequilibrium typically contain in the order of 10 genes, linkage
disequilibrium mapping and association studies with candidate
genes bring us close to the level of individual loci. These approaches
may be useful when pedigrees are small, as in human populations,
or when genotyped populations can be used by many researchers
for analysis of multiple phenotypes, as in A. thaliana. Several
challenging statistical issues remain for association studies in A.
thaliana. Population and pedigree structure can be incorporated into
analytical models
72
or homogeneous populations may be identified.
However, if ancestral populations have diverged for the trait of
interest, then statistical adjustment for population structure may
remove the very effects of interest
73
. Linkage disequilibrium
mapping and association studies also result in false negatives and
false positives
74
. Consequently, results from association studies
represent hypotheses that must be tested by independent
experiments
43
.
REVIEWS NATURE|Vol 441|22 June 2006
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must identify nucleotide polymorphisms with functional effects on
phenotypic differences. Such polymorphisms are also of great inter-
est to plant molecular biologists seeking to elucidate gene function
and genetic pathway structure
20
. Identification of natural variants is
particularly important for functional studies because some knockout
mutations may be lethal, or may lack detectable phenotypic effects
due to genetic redundancy
21
. These efforts will be greatly aided by
databases on genome-wide patterns of nucleotide polymorphism
3
,
gene expression
22
, and developmental phenotypes
23
.
The identification of natural polymorphisms controlling variation
in complex traits begins w ith screens of trait variation among
accessions. Once such variation is identified, the next step is to
identify polymorphic genomic regions (quantitative trait loci, or
QTL) associated with that variation. Recent advances in characteriz-
ing genome-wide polymorphism and population structure for a wide
range of A . thaliana ecotypes
3,15
may facilitate identification of
QTL through linkage disequilibrium mapping (Box 1). Recombinant
inbred lines (RILs) between divergent parental ecot ypes have already
proved extremely valuable for mapping QTL for a variety of eco-
logically important complex traits
20
. QTL of moderately large effect
have been identified in a number of studies, but chromosomal
regions with large phenotypic effects may actually contain multiple
linked QTL of smaller effect
24
. A substantial portion of genetic
variation for complex traits may actually correspond to polygenic
models of complex trait variation, with many genes o f small
effect
25,26
.
Recent advances in genomics make it possible to treat genome-
wide expression patterns as complex traits and screen for natural
variation in those patterns. Schmid et al.
22
studied expression of
22,000 genes in many developmental stages and tissues, providing
invaluable data on regulatory patterns in Arabidopsis and enabling
further functional
27
and evolutionary analyses. Patterns of gene
expression differ among Arabidopsis accessions
28,29
, and QTL influ-
encing cis-ortrans-regulatory polymorphisms can be identified
30
.
Cis-acting allele-specific transcriptional differences are apparently
common in Arabidopsis
30,31
and other organisms
32
. Progress in this
field requires experiments that relate transcriptional polymorphisms
to phenotypic variation at the whole-plant level.
One important lesson from QTL studies with A. thaliana is that the
expression of phenotypic differences between QTL alleles may
depend strongly on environmental conditions and genetic back-
ground. QTL–environment interactions are common; often, certain
QTL are expressed in some environments but not in others, or differ
in the magnitude of their allelic effects. Although such observations
are common in A. thaliana
33,34
, their molecular basis and relationship
to genotype–environment interactions at the whole-organism level
have rarely been elucidated. To date, antagonistic pleiotropy
—
in
which the alleles of a QTL change phenotypic rank across environ-
ments
35
—
seems to be rare in A. thaliana. Clearly, more work is
needed to understand the genetic basis of genotype–environment
interaction.
Epistasis, or interaction effects among different loci, is a funda-
mental force in many aspects of adaptive evolution
36
. At its simplest,
epistasis occurs when the genot ype at one locus influences the
magnitude of allelic effects at another lo cus. More intriguingly,
with sign epistasis the genot ype at one locus may reverse the direction
of allelic effects at another gene. There is now strong evidence that
both kinds of epistasis are important in A. thaliana
34,37–40
. In some
cases, the mechanisms of epistasis are known from functional
studies
41,42
. At the level of individual genes, sign epistasis influencing
juvenile growth rate (an important component of fitness) is caused
by genetic poly morphism at a serine/threonine protein kinase, and
patterns of nucleotide polymorphism suggest that balancing selec-
tion maintains elevated levels of genetic variation
25
. These obser-
vations suggest that epistasis may have a fundamental role in the
evolution of A. thaliana and other inbreeding species.
Once QTL regions have been identified, the next step is to find the
underlying genes and nucleotide polymorphisms causally associated
with trait variation. Rigorous standards of proof for determination of
the molecular basis of a QTL have been established
43
, and several
recent studies have used methods such as fine mapping and trans-
genic complementation to identify causal genes
25,44,45
. However, until
homologous recombination techniques for allelic replacement
become available for A. thaliana
46
, the variation introduced by
position effects may limit the power to detect minor allelic effects.
This is well illustrated by a study of the fitness effects of inserting a
transgene for Rpm1-mediated pathogen resistance
47
, where compari-
sons among five independent insertion lines found that fitness
differed by 37% among lines that varied only in the genomic location
of the transgene.
What sorts of molecular polymorphisms control quantitative trait
variation? Examples from A. thaliana span the full range of gene
function, including photoreceptor protein polymorphisms
44
, tran-
scriptio n factors
48
, cis-regulator y polymorphisms
30
, insertion/
deletion polymorphisms
42
, and copy-number variation in tandem
Box 2 | Sequence signatures
Until recently, cloning of QTL has been confined to laboratory model
systems, hence it has been impossible to measure the fitness effects
of QTL alleles in natural environments. As an alternative approach,
adaptive significance has been inferred from the sequence signature
of nucleotide polymorphism
5
. Population genetics theory can predict
patterns of nucleotide polymorphism on the basis of standard
neutral models for ideal, equilibrium populations. Statistical
hypothesis tests can then compare predictions from these standard
neutral models to observed variation at genes of interest. For
example, the figure shows ‘gene trees’ portraying the historical
relationship among alleles at a given locus. A typical selectively
neutral locus is shown on the left, with average levels of nucleotide
polymorphism. In contrast, balancing selection (centre) can
maintain high levels of variability for long periods of time. Such
polymorphisms are unusually old, and have accumulated high levels
of molecular variation. Finally, an advantageous mutation may out-
compete existing alleles in a ‘selective sweep’ (right), reducing
extant variation below neutral levels. Although these theoretical
predictions apply to ideal populations, non-standard or non-
equilibrium demographic conditions such as gene flow or changing
size
5
also influence allelic variation in real-world populations. With
data from only a single locus, statistical tests often cannot
determine whether differences between observed and predicted
patterns are due to natural selection, or instead reflect neutral
effects of demographic history. Fortunately, genome-wide patterns
of variation contain a signature of historical demographic processes,
because demography influences variation across the genome. In
contrast, the effects of natural selection are confined to the target
locus and adjacent regions. Consequently, putative natural selection
at genes of interest may be identified by comparison to a genome-
wide ‘empirical null distribution’ summarizing variability at many
loci, or by simulations based on plausible non-standard models.
Recently, several studies
3,4
have shown that variation in A. thaliana
does not conform to standard demographic models of ideal
populations. Instead, gene flow among populations, changing
population size, extinction, and recolonization evidently have
influenced polymorphism in A. thaliana.
NATURE|Vol 441|22 June 2006 REVIEWS
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© 2006 Nature Publishing Group
gene families
12
. However, current examples are insufficient to draw
generalizations about the importance of regulatory versus coding
polymorphisms, especially because the QTL that have been cloned so
far have larger than average effects, and may not be representative of
small-effect QTL.
Natural selection for complex traits
How does natural selection act on trait variation in the real world?
The native range of A. thaliana spans a broad range of climates and
habitats. A. thaliana has evolutionarily expanded its range to warmer
climates from the cool temperate ‘climate space’ inhabited by other
Arabidopsis species
49
. This climatic range expansion may result from
A. thaliana’s evolutionary transition to an annual life history from
the perennial strateg y shown by i ts close relatives. The annual
strategy may increase tolerance of warmer climates by allowing
plants to survive summer conditions as seeds rather than as juvenile
or adult plants. However, the annual strategy necessitates germinat-
ing and flowering during favourable growing conditions, and the
seasonal timing of these events varies across the climatic range of
the species. Natural populations of A. thaliana are thus likely to
experience very different selective pressures across the species range.
If geographic variation in climate has resulted in local adaptation, we
should expect genetic associations between the phenotype of an
accession and the climate in its site of origin.
How much natural variation exists for ecologically important
traits in A. thaliana? Experiments with geographically diverse eco-
types under common garden conditions reveal remarkable genetic
variation in many ecologically important traits
20,23,48,50,51
. Much less is
known about the phenology and demography of natural A. thaliana
populations in situ, but it is clear that the species shows variation in
life history timing across its range. In particular, there is a life history
polymorphism between winter annual ecotypes
—
which overwinter
as small vegetative rosettes and flower in spring
—
and rapid cycling
ecotypes
—
which germinate and flower in late summer and again in
spring to produce two generations per year (ref. 52). This poly-
morphism has been attributed to loss of a vernalization requirement
conferred by mutation at the major flowering time loci, FRIGIDA
(FRI)
42,53
and FLOWERING LOCUS C (FLC)
54
, w ith additional
variation due to other loci
23,48,51
.
Does the observed genetic variation among natural populations
represent adaptive differentiation in response to heterogeneous
natural selection? This hypothesis can be tested with several different
lines of evidence (Table 1). First, is trait variation associated with
geographical variation in climate or other ecological factors? Second,
is the degree of quantitative variation among populations greater
than expected on the basis of differentiation at neutral markers?
Third, do local genotypes have higher fitness than foreign genotypes
in reciprocal transplant experiments, and if so, is this ‘home-court
advantage’ attributable to selection favouring the local phenotype of
the candidate trait? The first two questions have recently been
addressed by quantitative genetic studies in common garden
environments, and provide some support for the adaptive differen-
tiation hypothesis. However, the third question will require ev idence
from reciprocal transplant experiments and field studies of selection.
Several studies have detected latitudinal clines in A. thaliana growth
and morphology, seedling traits, flowering time, vernalization sensi-
tivity, and circadian period
23,55–58
. Such gradients in complex traits may
provide evidence of local adaptation, especially if the direction of
the cline is consistent with functional arguments
58
. However, clinal
variation may also result from non-adaptive phenomena such as
isolation by distance or admixture between two divergent founder
populations. Therefore, geographic tests of trait adaptation are most
compelling when combined with other forms of evidence.
If population differentiation in a trait is adaptive, the degree of
quantitative genetic differentiation in the trait among populations
should be greater than the genetic differentiation among populations
in neutral molecular markers
18
. (Typically, the proportion of genetic
variation found among populations for phenotypic traits and neutral
molecular markers is quantified by Q
st
and F
st
, respectively.) Using
this approach, Le Corre
18
measured trait variation within and among
natural populations in France. The Q
st
for bolting time was signifi-
cantly higher than the overall F
st
estimated from neutral molecular
markers, suggesting adaptive divergence among populations in
reproductive timing. Moreover, the F
st
for functional polymorphism
at the principal flowering time gene FRI was also significantly higher
than F
st
at marker loci, suggesting adaptive differentiation at that
locus. Because FRI confers a vernalization requirement, and is known
to be associated with flowering time in non-vernalized plants, these
Table 1 | Evidence for adaptation
Method Known
gene?
Advantages Disadvantages Reference Time
frame
Transgenic comparison
of candidate allele effects
Yes The gold standard for functional
verification and fitness
consequences
Transgene position effects
Regulatory complications with field
trials
47 Current
QTL, RILs, NILs No Does not require known gene
Modest regulatory requirements
Effects may be confounded with
flanking genes
40 Current
Sequence signature Yes Capable of detecting very weak
selection
Does not require
phenotypic information
Must control for demographic
history
Phenotype experiencing selection is
unknown
5 Historical
F
st
/Q
st
No F
st
can be calculated from
relatively few neutral loci
Does not require genome-wide
molecular markers
Difficult to detect local adaptation
when F
st
is large
18 Historical
Hitchhiking mapping No May localize chromosomal region
experiencing local adaptation
Phenotype experiencing selection
is unknown
75 Historical
Genotype–environment
association
No Can be applied when causal genes
are unknown
May be confounded with gene flow
or admixture
58 Historical
Multivariate selection
analyses
No Can be applied when causal genes
are unknown
May be confounded with unmeasured
traits
61 Current
Reciprocal transplants No With proper replication, may detect
local adaptation
Can be applied when causal genes
are unknown
Requires access to original populations
and environments
Further experiments needed to establish
mechanism
59 Historical and
current
Abbreviations: QTL, quantitative trait loci; RILs, recombinant inbred lines; NILs, near-isogenic lines; F
st
, the proportion of molecular marker polymorphism found among populations; Q
st
,the
proportion of quantitative genetic variation found among populations.
REVIEWS NATURE|Vol 441|22 June 2006
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results suggest that the adaptive divergence of flowering time occurred
through selection for loss of FRI function in certain populations.
Common garden studies may provide evidence for adaptive
population differentiation in complex traits, and suggest hypotheses
about selective mechanisms for such differentiation. However, direct
support for the local adaptation hypothesis requires reciprocal
transplants between natural populations
59
, and selective mechanisms
are best tested by measuring natural selection on traits of interest in
such experiments. Although this approach has proved to be very
powerful in other plant species, it has rarely been attempted for
A. thaliana, and evidence for local adaptation has been equivocal
60
.
A reciprocal-transplant approach could be very valuable for testing
hypotheses about local adaptation to climate across the native range
of A. thaliana.
Although direct experimental tests of local adaptation are still
lacking for A. thaliana, several field experiments provide strong
evidence for real-time natural selection on complex traits and specific
loci. Multivariate selection analysis
61
quantifies how natural selection
acts on variation in complex traits. Such studies are most valuable
when combined with ecological manipulations to test hypotheses
about the causes of selection
62
. For example, Donohue et al.
63
demonstrated geographical differences in selection on germination
timing for seeds of the same genot ypes experimentally dispersed in
Rhode Island and Kentucky, as well as seasonal differences in
selection between seeds dispersed in spring and autumn.
How does natural selection on complex traits act on specific loci?
Recent field experiments with RILs have identified QTL influencing
fitness in different environments
40,64,65
. The same set of lines showed
largely different QTL for fitness in Georgia
40
, North Carolina, and
Rhode Island
65
, suggesting that natural selection acts on different
genomic regions in different geog raphic locations and seasonal
environments. These studies also revealed pervasive epistatic selec-
tion. For example, Malmberg and colleagues
40
found epistatic QTL to
be more common and more important than non-epistatic QTL, and
found a high frequency of sign epistasis for fecundity. Such epistatic
interactions can maintain genetic variation and constrain evolution-
ary responses to natural selection
36
, and may provide a possible
mechanism for the maintenance of polymorphism in A. thaliana.
These studies could not test hypotheses about local adaptation, as
the parents of the RILs were not native to the field sites. Rather, they
provide insights into how natural selection will act on the segregating
variation in different novel environments, a potentially relevant
scenario for this colonizing species. Such experiments also can test
whether fitness QTL co-localize with QTL for complex traits experi-
encing natural selection, thus provi ding insights into selective
mechanisms
64
. The next step is to take RILs from locally adapted
parental ecotypes and conduct selection experiments with the RILs in
the parental sites of origin. Such experiments can elucidate the selective
mechanisms and specific loci contributing to local adaptation
66
.
Near-isogenic lines (NILs) containing alternate alleles of poly-
morphic candidate genes provide another promising tool for testing
hypotheses about how selection acts on polymorphisms in ecological
time. Such studies will be particularly useful for polymorphisms that
show the molecular signature of balancing selection in genes of
known ecological function. For example, R-genes in A. thaliana
confer resistance to pathogens, and are often polymorphic for resistant
or susceptible alleles, with evidence for balancing selection at the
molecular level
13,67,68
. Experiments with NILs
69
and pairs of transgenics
that differed in the presence or absence of a resistant allele
47
were able to
demonstrate fitness costs of resistance allel es, which provide an
ecological mechanism for the maintenance of these polymorphisms.
This approach may be valuable for future studies of the selective
mechanisms acting to maintain variation at other candidate loci.
Future prospects
Future advances in our understanding of A. thaliana natural vari-
ation depend, in part, on improvements in resources and technology.
Among the highest priorities are expanded collections from well-
characterized environments, as well as possible undisturbed popu-
lations from Eurasia. On the technical side, the greatest need is for
straightfor ward protocols to reduce transgene position effects, such
as gene targeting
46
or alternative approaches
47,70
.
Arabidopsis research is poised to address fundamental questions in
evolution and ecology, including: What is the role of epistasis, and
how does it influence the evolution of developmental pathways? How
do ecological processes influence balancing selection within and
among populations? What are the frequencies and effects of QTL
alleles, and how is this influenced by evolutionar y forces? What are
the ecological and molecular mechanisms of local adaptation within
the native range of A. thaliana? How do real-time ecological processes
influence adaptive evolution in introduced and invasive populations?
As the field matures, research will focus increasingly on related
species, which will greatly improve our understanding of the genetic
basis and evolutionar y mechanisms of speciation.
Equally as important, Arabidopsis biology encourages (and
requires) interdisciplinary research and training. A new synthesis
of functional genomics with evolution and ecology will benefit each
component discipline, and will bring fundamental advances in our
understanding of biological mechanisms and processes. Such training
provides an essential component of science education for the future.
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Acknowledgements We thank M. Noor, M. Nordborg and our collaborators and
laboratory members for discussion and comments. T.M.-O. and J.S. were
supported by Duke University and the National Science Foundation,
respectively.
Author Information Reprints and permissions information is availabl e at
npg.nature.com/reprintsandpermissions. The authors declare no competing
financial interests. Correspondence should be addressed to T.M.-O.
(tmo1@duke.edu).
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