Genome-Wide Patterns of Nucleotide
Polymorphism in Domesticated Rice
Ana L. Caicedo1[¤a, Scott H. Williamson2[, Ryan D. Hernandez2, Adam Boyko2, Adi Fledel-Alon2¤b, Thomas L. York2,
Nicholas R. Polato3, Kenneth M. Olsen1¤c, Rasmus Nielsen2¤d, Susan R. McCouch3, Carlos D. Bustamante2*,
Michael D. Purugganan1,4,5*
1 Department of Genetics, North Carolina State University, Raleigh, North Carolina, United States of America, 2 Department of Biological Statistics and Computational
Biology, Cornell University, Ithaca, New York, United States of America, 3 Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of
America, 4 Department of Biology, New York University, New York, New York, United States of America, 5 Center for Comparative Functional Genomics, New York University,
New York, New York, United States of America
Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more
people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild
ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics
that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide
polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed
several alternative models to explain contemporary patterns of polymorphisms in rice, including a (i) selectively
neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and
(iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been the dominant
demographic model for domesticated species, cannot explain the derived nucleotide polymorphism site frequency
spectrum in rice. Instead, a bottleneck model that incorporates selective sweeps, or a more complex demographic
model that includes subdivision and gene flow, are more plausible explanations for patterns of variation in
domesticated rice varieties. If selective sweeps are indeed the explanation for the observed nucleotide data of
domesticated rice, it suggests that strong selection can leave its imprint on genome-wide polymorphism patterns,
contrary to expectations that selection results only in a local signature of variation.
Citation: Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, et al. (2007) Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS
Genet 3(9): e163. doi:10.1371/journal.pgen.0030163
Domestication is a complex, cumulative evolutionary
process in which human use of organisms leads to morpho-
logical and/or behavioral changes distinguishing domesti-
cated species from their wild ancestors [1,2]. Beginning with
Charles Darwin [3,4], there has been strong interest in the
study of domestication of crop species as a means of
understanding the nature of selection. Moreover, domestica-
tion and the development of agriculture are arguably the
most important technological innovations in human history
. Crop plant domestication was the linchpin of the
Neolithic Revolution 10,000–12,000 years ago, in which
hunter-gatherer groups transitioned into sedentary agricul-
tural societies that gave rise to current human cultures .
With domestication came the availability of food surpluses,
and this agricultural development led to craft specializations,
art, religious and social hierarchies, writing, urbanization,
and the origin of the state .
One of the earliest domesticated crop species is cultivated
Asian rice, Oryza sativa L., which has become the world’s most
widely grown crop and has also assumed the stature of a key
model system in plant biology. Rice consumption constitutes
about 20% of the world’s caloric intake, and in Asian
countries, where over half of the world’s population lives,
rice often represents over 50% of the calories consumed .
Because of its small genome size, rice has been the first crop
plant to have its whole genome sequenced [8–10].
A wealth of morphological, physiological, and ecological
variation exists within cultivated Asian rice, reflected in the
large number of recognized cultivars or strains [11,12]. Two
main rice varietal groups, O. sativa indica and O. sativa japonica,
have been recognized since ancient China . Although
phenotypic distinctions between these groups is not always
straightforward, indica varieties tend to be found throughout
Editor: Gil McVean, University of Oxford, United Kingdom
Received February 20, 2007; Accepted August 6, 2007; Published September 28,
A previous version of this article appeared as an Early Online Release on August 6,
Copyright: ? 2007 Caicedo et al. This is an open-access article distributed under
the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original author
and source are credited.
Abbreviations: AIC, Akaike information criterion; GOF, goodness-of-fit; SNP, single
nucleotide polymorphism; STS, sequence-tagged site(s)
* To whom correspondence should be addressed. E-mail: email@example.com (CDB);
[ These authors contributed equally to this work.
¤a Current address: Department of Biology, University of Massachusetts, Amherst,
Massachusetts, United States of America
¤b Current address: Department of Human Genetics, University of Chicago,
Chicago, Illinois, United States of America
¤c Current address: Department of Biology, Washington University, St. Louis,
Missouri, United States of America
¤d Current address: Centre for Bioinformatics, University of Copenhagen, Denmark
PLoS Genetics | www.plosgenetics.orgSeptember 2007 | Volume 3 | Issue 9 | e163 1745
the tropical regions of Asia and are primarily grown in
lowland conditions, while japonica types are differentiated
into tropical japonica, distributed in upland tropical regions,
and temperate japonica, a recently derived group cultivated in
temperate regions [11,13,14]. Additional variety groups
include aus, drought-tolerant rice from Bangladesh and West
Bengal, and aromatic, fragrant rice from the Himalayan range
[14,15]. All rice varieties have a predominantly self-fertilizing
mating system . Both morphological and isozyme data
have established that O. rufipogon Griff., a partially outcrossing
species native to southern Asia, is the wild ancestor of
domesticated rice .
In this paper, we describe the levels and patterns of DNA
sequence polymorphism across the rice genome and that of
its wild ancestor, O. rufipogon. To our knowledge this is the
first genome-wide characterization of sequence variation in
domesticated Asian rice, and we show that rice contains a
unique pattern of excess high-frequency derived single
nucleotide polymorphisms (SNPs) that has not been reported
in other species. We develop four models to explain patterns
of genetic variation in O. sativa and O. rufipogon, including a
simple selectively neutral bottleneck model that has been
previously thought to be the dominant demographic force
shaping levels of nucleotide variation in crop species. We
demonstrate that this simple bottleneck model is inadequate
to explain the origin of domesticated rice. We conclude that
either positive selection has made a significant impact on
genomic polymorphism patterns, or that domestication
involved an extremely severe bottleneck (;99.5% reduction)
coupled with gene flow among modern varieties and between
domesticated rice and its wild ancestor.
Nucleotide Variation in the Rice Genome
To assess levels and patterns of polymorphism in the rice
genome, we sequenced one hundred eleven randomly chosen
gene fragments (sequence-tagged sites or STS) in a diverse
panel of Oryza accessions, including 72 from O. sativa and 21
from O. rufipogon (Tables S1 and S2). Average silent
(synonymous and noncoding) site nucleotide diversity (hp)
across all sampled loci in O. sativa is approximately 3.20 3
10?3(Table 1). Levels of polymorphism in the wild ancestral
species, O. rufipogon, are predictably higher than rice, with a
mean silent hp of 5.19 3 10?3(Table 1). These levels of
polymorphism are lower than those observed for maize, a
domesticated outcrossing species , and Arabidopsis thaliana,
a selfing, wild species [17,18].
To determine if any genetic differentiation due to
population structure among rice groups is evident in these
STS sequences, we used the Bayesian clustering program
STRUCTURE . The highest likelihood obtained was with a
model specifying K ¼ 7 groups (Figure 1; Table S1). Five
groups occur within O. sativa and correspond to the
traditional variety designations, as described previously .
Evidence of some limited geographical population structure
is also observed in O. rufipogon (Figure 1; Table S1). Neighbor-
joining analysis of the concatenated STS sequences (Figure
S1) revealed two distinct clusters within cultivated rice; one
comprises a tropical japonica, temperate japonica, and aromatic
rice lineage, and another consists of aus and indica rice. The
apparent monophyly of these major groups is consistent with
at least two domestication events in rice [14,20–24]. The
nesting of the aromatic and the temperate japonica variety groups
within tropical japonica suggests the first two groups originated
from secondary divergence events from the latter, although
Table 1. Average Diversity Measures in Oryza spp. across 111 STS Regions
StatisticCategoryO. sativaO. rufipogon
aus indica japonicatemperate japonicatropical japonica
hpbper KbTotal sites
aValues for the aromatic group are based on 110 STS.
bAverage nucleotide diversity across all sequenced STS fragments.
cSilent site estimates include synonymous and noncoding sites.
dAverage values for Watterson’s estimate of theta across all sequenced STS fragments.
eAverage Tajima’s D across all sequenced STS fragments.
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Polymorphism in Domesticated Rice
Domesticated Asian rice is one of the oldest and most important
crops in the world. Two main rice evolutionary lineages have been
identified, and are thought to have been independently domes-
ticated in Asia. We have examined patterns of DNA sequence
variation in the genomes of rice and its wild ancestor to make
inferences about the origin of domesticated rice. Population
bottlenecks (a reduction in the size of the founding population) in
the evolutionary transition from wild to cultivated species has long
been thought to be the dominant force shaping patterns of
molecular evolution during domestication. We find that the
nucleotide variation patterns in rice are inconsistent with a simple
bottleneck model. Rice genetic variation, however, can be explained
by either a model that incorporates both a bottleneck and migration
among rice variety groups, or a model that incorporates a
bottleneck and multiple rounds of artificial selection on rice.
Selection by humans is believed to have played an important role
during crop domestication, and these results may suggest that
strong, recurrent selection can leave a signal that can be observed
throughout the genomes of domesticated species.
the lack of support for tropical japonica branches does not
exclude other possible divergence scenarios (Figure S1). Indica
and aus relationships, on the other hand, are consistent with
rapid divergence after domestication or separate domestica-
tion events from the same ancestral gene pool. Within-group
SNP levels of cultivated rice are lower than those of the whole
species (Table 1), with subpopulations harboring between
19% (temperate japonica) and 43% (indica) of the polymorphism
of O. rufipogon. Assuming separate domestication events, the
japonica clade contains 42% and the indica clade contains 48%
of the diversity levels found in O. rufipogon.
The Derived Site-Frequency Spectrum is U-Shaped in O.
Because of the strong population structure evident in our
rice sample, it is necessary to assess patterns of variation
separately for each group when making inferences about the
evolutionary dynamics of domestication. Indica and tropical
japonica represent the most widely grown cultivars for each of
the separate domestication events, and we limited our
characterization of polymorphism patterns to these two
groups. We examined the frequency spectrum of segregating
sites within loci using Tajima’s D , and found that O.
rufipogon and the two main rice subspecies show an excess of
rare alleles, as evidenced by the biased distribution of
Tajima’s D toward negative values (Figure S2; Table 1). Crops
are expected to have gone through a population bottleneck
during domestication, as only a limited number of founding
individuals were brought into cultivation. The distribution of
Tajima’s D in the domesticated rice varieties is inconsistent
with a recent bottleneck, however, as these should reduce
levels of low-frequency variants and bias measures of Tajima’s
D toward positive values. It is possible that subsequent
population expansion, due to the spread of rice agriculture,
could be responsible for the over-representation of rare
alleles segregating in domesticated rice varieties, or selection
may have played a role.
We further examined the derived site-frequency spectrum
across SNPs (i.e., the fraction of derived polymorphisms
present at various frequencies within a group) in indica and
tropical japonica. To infer ancestral alleles for each SNP, we
used as an outgroup O. meridionalis, a species believed to have
diverged from O. sativa ;2 million years ago . In each O.
sativa variety we observed a large number of high-frequency
derived mutations (i.e., derived SNPs above 70% frequency in
the population) leading to a U-shaped frequency distribution
(Figure 2); this type of pattern has not been reported at the
genomic level in any other species.
Possible explanations for the excess of high-frequency
derived SNPs in O. sativa include the misidentification of
ancestral states due to shared polymorphism with O.
meridionalis, or the occurrence of multiple mutations at given
sites since divergence from O. meridionalis. However, both
misidentification of derived alleles and multiple hits would be
expected to also affect the site-frequency spectrum of O.
rufipogon, which is not observed (Figure 2). This suggests that
the O. sativa derived site-frequency distribution is a result of
the domestication process. Furthermore, derived alleles at
high frequency in the O. sativa varieties occur primarily at low
to intermediate frequency in O. rufipogon, suggesting that such
alleles have only recently increased in frequency (Figure S3).
We also checked the ancestral state calls in O. sativa using
the African wild rice O. barthii. Although O. barthii is more
closely related to O. sativa than is O. meridionalis, if we assume
that both wild species share ancestral polymorphisms with
domesticated rice, the possibility that we always identified the
same alternative allele as derived in our sample should be low.
Using this approach, we find that 88% of our ancestral SNP
calls in indica and 86% in tropical japonica matched in O. barthii
and O. meridionalis. Even when using only the matched calls
(which is a very conservative criterion, since it does not take
into account drift and/or fixation processes in O. barthii), the
site frequency spectrum in O. sativa varieties remains U-
Figure 1. Estimated Population Structure for 97 Accessions of O. sativa and O. rufipogon from 111 STS Loci
Vertical bars along the horizontal axis represent each Oryza accession; for all accessions, the proportion of ancestry under K ¼ 7 clusters that can be
attributed to each cluster is given by the length of each colored segment in a bar.
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Polymorphism in Domesticated Rice
An excess of high-frequency derived SNPs is often
interpreted as a result of genetic hitchhiking during recent
selective sweeps . Because the site-frequency spectrum in
rice varieties is observed from randomly selected loci, and the
loci contributing high-frequency derived SNPs are distrib-
uted across the genome (Figure S4), this pattern suggests that
strong linkage to positively selected mutations occurred
within most of the genome. However, demographic forces
may have also played a role in shaping the rice genomes. We
developed several demographic models and a multiple
selective sweeps model to test which evolutionary processes
may best explain the observed patterns of polymorphism in
Demographic Models for Rice Domestication: A Neutral
Population Bottleneck Model
The most widely accepted demographic model for crop
domestication is a neutral bottleneck model [27–29]. In this
model, rice domestication is assumed to be a result of recent
population divergence, with one of the two daughter
populations experiencing a reduction in population size at
divergence associated with the founder effect at the time of
domestication, followed by population growth as cultivation
of the crop increases. To fit this model to our data, we used a
diffusion-based approach [30–32] to predict the pattern of
allele frequencies in domestic and ancestral populations
under selective neutrality.
Details of the inference procedure can be found in the
Materials and Methods section. The composite-likelihood
function we employed uses the reduction in diversity
observed in either of the domesticated rice subspecies and
the shift in allele frequency distribution to estimate four
parameters: the time back until the start of domestication
(s1), duration of the bottleneck (s2), ratio of current
population to ancestral population size (m2), and relative size
of the bottleneck population to the ancestral population (mb).
The duration of the bottleneck was assumed to be 25% of the
time back until domestication (s2¼ 0.25 3 s1), which is
consistent with archeological data suggesting it took ;3,000 y
from the time of initial cultivation (;12,000 y ago) until the
appearance of domesticated rice grains [33,34].
Bottleneck parameter estimates for indica and tropical
japonica are broadly comparable, with a slightly more severe
bottleneck in tropical japonica (Table 2). Assuming the time
back to the beginning of domestication for both variety
groups was ;12,000 y , we can independently derive
estimates of the current O. rufipogon effective population size,
Nrufi, using the relationship s132Nrufi¼12,000 (because s1is
scaled by 2Nrufi). From the indica analyses, Nrufiis equal to
12,000/(2 3 0.1044) ¼ 57,471, and from the tropical japonica
analyses is equal to 12,000/(2 3 0.0508) ¼ 118,110 (this exact
Figure 2. The Observed Marginal Derived Site-Frequency Spectra of Noncoding and Synonymous SNPs for Two Population Pairs: indica and O.
rufipogon and tropical japonica and O. rufipogon
To accommodate SNPs with missing data, all spectra are plotted as the expected site frequency spectrum in a subsample of the data of size n ¼ 16.
Table 2. Maximum Likelihood Estimates for Demographic
Parameters of the Bottleneck and Bottleneck plus Migration
Models in indica, tropical japonica, and O. rufipogon
0.5 3 M 3 m2d
as1is time back to the start of domestication period (;12,000 y before present) scaled by
bm2 is the ratio of the effective population size of current population to ancestral
cmbis the ratio of the effective population size of bottleneck population to ancestral
population (i.e., N/Nrufi).
d0.5 3 M 3 m2¼ 2Nm is the number of migrants arriving per generation into the indica,
tropical japonica, and O. rufipogon populations after the bottleneck ends (maximum
composite likelihood estimate of migration rate, M ¼ 4Nrufi¼ 7.0).
eBottleneck model was evaluated by Poisson random fields analysis of site frequency
fBottleneck þ migration model was evaluated by composite likelihood analysis of
marginal site-frequency spectrum using coalescent simulations.
gWithin m2and mbcolumns, these parameters are set to be equal to one another in
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Polymorphism in Domesticated Rice
value of Nrufi is important in scaling all of the estimated
parameters into years and number of individuals). The indica-
derived Nrufi estimate implies bottleneck and current
estimated population size (Ne) for indica of (mb3 Nrufi) ¼
1,413 and (m23 Nrufi) ¼ 40,229 respectively. The second
estimate suggests a bottleneck and current Nesizes for tropical
japonica of (mb3 Nrufi) ¼ 1,334 and (m23 Nrufi) ¼ 46,889,
The differences in estimates of Nrufifrom each analysis
could be attributable to differences in the founding pop-
ulation of each variety group or differences in the timing of
each domestication event. We note, however, that a bottle-
neck model conditioned on coincident domestication for
indica and tropical japonica (equal s1values) differs only by 1.8
log likelihood units (unpublished data), suggesting that equal
timing of domestication is likely to have occurred. An
independent estimate of Nrufi can be found by using the
estimated scaled population silent mutation rates (hW¼4Nrufi
l ¼ 5.42 3 10?3per bp; Table 1) and the observation that the
O. rufipogon site-frequency spectrum is consistent with that of
a population of long-term constant size (Figure 2). Assuming
a neutral mutation rate of 10?8per bp, yields a point estimate
of Nrufi¼ 135,500, which is slightly higher, but close to the
estimates found by conditioning on the start of domestica-
Demographic Models for Rice Domestication: A Complex
Model Incorporating Subdivision, Bottlenecks, and
It is important to note that population bottlenecks alone
would not generate the strong excess of high-frequency
derived alleles and strong U-shaped site-frequency spectrum
observed in O. sativa (Figure 2) . In order to explain this
aspect of the data, we considered several demographic
models that included ancient subdivision in the ancestor of
rice, a bottleneck at the time of domestication for each
domesticated varietal group, and limited gene flow between
the independently domesticated rice groups indica and tropical
japonica. Ancient, strong subdivision is not evident in our O.
rufipogon sample (Figure 1); Fst between Chinese and non-
Chinese O. rufipogon is low, about 0.16, and no interior modes
are evident in the site-frequency spectrum of O. rufipogon, as
expected under subdivision. However, it is possible for
limited gene flow in O. rufipogon to lead to some differ-
entiation of allele frequency between groups, but not so
much that it would have a strong effect on a combined O.
rufipogon sample. Furthermore, the population bottlenecks
induced by independent domestication events could amplify
any allele frequency differentiation between indica and tropical
japonica, and limited gene flow between these two groups
could introduce ancestral alleles into each population,
causing mutations previously fixed in one group to be
observed as high-frequency derived alleles in the other.
To test the effect of ancestral population substructure
within O. rufipogon prior to the domestication of the two O.
sativa groups, we fit the parameters of a complex demo-
graphic model to our data using a composite likelihood
technique (see Materials and Methods). We began by
exploring a model with seven demographic parameters,
which consists of O. rufipogon being subdivided into two
demes of equal size, sharing on average MR migrants per
generation. Current-day indica varieties are descended from
one of these demes, while tropical japonica varieties descend
from the other. During the domestication process, each
population underwent a bottleneck that began s1generations
ago (in units 2Nrufi) and had severity mb (the ratio of the
reduced population size to the ancestral size). After s2¼ 0.25
3 s1generations (;3,000 y), both indica and tropical japonica
partially recovered, instantaneously reaching a fraction tI
and tJof the ancestral size, respectively. Contemporary gene
flow (since domestication) between tropical japonica, O.
rufipogon, and indica is captured by the last parameter, the
average number of migrants per generation between these
demes (MS). This model was conceived because it incorpo-
rates key demographic features of rice or crop domestication
(e.g., bottlenecks, two domestication events) and could
conceptually generate the observed derived SNP site fre-
In preliminary analyses, we found that the migration rate
(MR) between the two ancestral O. rufipogon demes was very
large, with the marginal likelihood surface for this parameter
near its maximum value whenever MR. 7. This is consistent
with our observations of limited population structure in O.
rufipogon (above), and we therefore discarded ancestral
population structure as a main contributor to the patterns
observed in our dataset, and simplified the demographic
model to consider only a single ancestral population from
with both indica and tropical japonica derive (with migration
rates among the three remaining demes, MS¼ 4Nrufim). This
assumption reduced the computational complexity, so that
the remaining parameters could be estimated via a grid
search using an initial size of over 2,000 points with 1,000,000
coalescent simulations per point. The resulting model (which
we refer to as the bottleneck plus migration model) has five
free parameters with composite maximum likelihood esti-
mates of MS¼ 7.0 (migration between demes), mb¼ 0.0055
(domestication bottleneck size), mI¼ 0.27 (ratio of indica to O.
rufipogon Ne), mJ¼ 0.12 (ratio of tropical japonica to O. rufipogon
Ne), and s1¼ 0.04 (start of domestication in units of 2Nrufi)
(Table 2). It is important to note that coalescent simulations
scale the migration based on population size, so the number
of migrants entering into the tropical japonica population is
smaller (0.5 3 M 3 mJ¼ 0.42), than into indica (0.5 3 M 3 mI¼
0.945), and O. rufipogon (0.5 3 M ¼ 3.5).
In Figure 3, we report the profile composite-likelihood
contours for the three key demographic parameters in the
bottleneck plus migration model: migration rate, start of the
bottleneck, and severity. The figure is constructed by holding
two parameters fixed at a given point in the (x,y) plane,
optimizing over the third parameter, and reporting the
maximum likelihood attained for the (x,y) point (due to
computational limitations the figure was constructed holding
the ratio of current-day indica and tropical japonica populations
at their maximum composite-likelihood estimates). We note
that the three parameters are moderately to strongly
correlated, but only a restricted set of values in high
dimensional space is consistent with the data. These solutions
all include: a very strong bottleneck (.99% reduction), high
rates of migration within and between domesticated and wild
populations of Asian rice (M . 5), and current-day effective
population sizes for cultivated rice that are substantially
smaller than those seen in the ancestral population. We also
note that the model solutions show a positive correlation
between size of bottleneck population and timing of the
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Polymorphism in Domesticated Rice
bottleneck, a negative correlation between size of the bottle-
neck and migration, and a negative correlation between
migration and timing (consistent with the ;2-fold difference
in the estimated time of the bottleneck between the model
with migration and the model without).
As can be seen in Figure 4, the expected site-frequency
spectrum under the best fitting bottleneck plus migration
model matches the observed frequency distributions fairly
well for both O. rufipogon as well as indica, but not as well for
tropical japonica. As expected, the total number of SNPs in
each of the three populations is predicted quite well by the
model. We quantified the fit of the model to the observed
data using a modified Pearson Chi-square goodness-of-fit
(GOF) statistic, and found that the best-fitting complex
demographic model is an excellent fit to the marginal indica
(GOFI¼20.26, p¼0.72) and O. rufipogon site-frequency spectra
(GOFR¼ 7.57; p ¼ 0.99), and an adequate fit to the tropical
japonica site-frequency spectrum (GOFT¼37.83, p¼0.22). One
interesting observation is that the demographic model
underpredicts the excess of high-frequency derived alleles
observed in tropical japonica—a potential indication of recent
positive selection. Given that artificial selection was probably
quite strong and frequent during and after domestication, we
further explored models that incorporate selection during
the domestication process of O. sativa.
Selection Models for Rice Domestication
Since strong selection is known to accompany crop
domestication, we developed two alternative models incor-
porating multiple selective sweeps to explain the unusual
polymorphism patterns in indica and tropical japonica. In a
neutral locus linked to a single, recent selective sweep, let fibe
the probability of observing a neutral mutation segregating at
frequency i in a sample of size n, conditional on the locus
being variable. An expression for fihas been derived  and
further extended [37,38], and includes the genomic distance d
(measured in bp) between neutral and selected loci, a
compound parameter a, which represents the combined
contributions of recombination, selection, and population
size, and the ‘‘background’’ allele frequency distribution (i.e.,
the expected site-frequency spectrum for loci unlinked to a
These results for a single sweep can be used to predict the
site-frequency spectrum at randomly chosen loci if multiple
sweeps have recently occurred. Assuming that selective
sweeps occur at random positions in the genome at a density
of j sweeps per bp, the distance between a random neutral
locus and the nearest sweep will be approximately exponen-
tially distributed with mean 1/(2j). Define the function /i(d, a,
j) to be the probability of observing i copies of a neutral
mutation in a sample of n chromosomes, given that a sweep
occurred at a distance d bp away with compound parameter a
, and background site-frequency spectrum q. By integrat-
Figure 3. Contours of Composite Profile Log-Likelihood Surface under
the Bottleneck and Migration (i.e., ‘‘Complex Demography’’) Model for
Three Key Demographic Parameters
Parameters include bottleneck severity, migration rate among demes
(4Nm), and s1(time back until start of domestication scaled in units of
2Nrufi). The maximum composite-likelihood estimate of the parameters is
denoted by a red filled circle.
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Polymorphism in Domesticated Rice
ing over the distance between the sampled locus and the
unknown target of the sweep, the marginal probability, Pi, of
observing a randomly chosen SNP at frequency i in a sample
of n chromosomes is a function of j, a, and q :
This probability can be used to calculate the composite
likelihood of the data and estimate the parameters j and a
(see Materials and Methods). It should be noted that this
equation assumes that the neutral locus is affected only by the
nearest selective sweep.
We considered two distinct models. The first is a model in
which strong selection is the only force that has acted in
domesticated rice populations, and uses the normalized O.
rufipogon site-frequency spectrum as the background fre-
quency distribution. The second, a bottleneck plus sweeps
model, allows multiple selective sweeps to affect patterns of
variation immediately following a population size change.
The background site-frequency spectrum in the latter case
can be approximated using the predictions of a simplified
neutral bottleneck model. The bottleneck plus sweeps model
incorporates the sweep density j, the compound parameter a
(the combined contributions of recombination, selection, and
population size), and a bottleneck severity parameter m.
The likelihood surfaces for both the pure selection and the
bottleneck plus sweeps model in rice each contains a long
ridge where different parameter combinations have almost
equally high likelihoods, implying that a model with high
sweep density and relatively weak selection is just as likely as a
model with low sweep density and strong selection (Figure 5).
For both models, the ridge of maximum likelihood is shifted
to the right in tropical japonica, indicating that for a given
value of the selection severity parameter a, the sweep density
in tropical japonica is estimated to be twice that in indica.
Sweep density is confounded with selection strength due to
the effect of a mating system change on recombination rate.
In domesticated rice, the transition to selfing likely occurred
simultaneously with the sweeps, making it difficult to
disentangle the recombination rate and selfing parameters.
Under a recent selective sweep in a randomly mating
population, the compound parameter a ’ rs?1ln(2N), where
r is the per-basepair recombination rate, s is the selection
coefficient and N is the population size . In a partially
selfing population such as domesticated rice, however, both
effective recombination rate and population size are affected
by selfing rate. While the rate of coalescence (and hence the
effective population size) is at most doubled by the rate of
selfing, the rate of recombination can be radically altered. An
expression for effective recombination rate is r(1?r/[2?r]),
where r is the selfing rate . For domesticated rice,
estimates of selfing rates are typically ;0.99 , resulting in
a reduced recombination rate by approximately 10?3. If we
assume 400 selective sweeps occurred in the rice genome
since domestication (j¼10?6), we estimate that a ¼2310?12
for indica. With r¼10?9recombination events per generation
per base pair and ln(2N) ’ 10, this estimate of a corresponds
to an unreasonably high estimate of a 5,000-fold fitness
advantage. Substituting an effective recombination rate of
10?12(corresponding to a reduced effective rate due to
selfing), we find more reasonable values for the strength of
selection for the selective sweeps, with s ’ 5. This example
illustrates how high selfing rates can amplify the signal of
selection and contribute to the pattern of polymorphism in
the rice genome.
Comparing Models to Explain Patterns of Nucleotide
Polymorphism in Rice
Visually, it appears both the bottleneck plus sweeps model
and the bottleneck plus migration model predict the site-
frequency spectrum of domesticated rice better than the
bottleneck model alone (Figure 4) or the pure selection model
(unpublished data). To compare likelihoods and determine
which model best fits the data, we used the Akaike
information criterion (AIC) . Since SNPs in our dataset
are linked, we used a composite likelihood function and
Figure 4. Observed and Expected Derived Site-Frequency Spectra under Various Models
The observed derived site-frequency spectrum for (A) indica and (B) tropical japonica, along with the expected site-frequency spectrum under the
simple bottleneck, bottleneck plus migration demography, and bottleneck plus sweeps models. (C) Observed site-frequency spectrum for O. rufipogon
and expected frequencies using a standard neutral model and a bottleneck plus migration model.
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Polymorphism in Domesticated Rice
simulations to assign p-values to the observed AIC statistic
(see Materials and Methods).
For indica, the bottleneck plus sweeps model is significantly
better than the neutral bottleneck model (K ¼ ?17.18, p ,
0.05) as is the bottleneck plus migration model (K¼?14.19, p
, 0.05). For tropical japonica, we also reject the neutral
bottleneck model in favor of both the bottleneck plus sweeps
model (K ¼ ?56.88, p , 0.01) and the bottleneck plus
migration model (K¼?53.60, p , 0.01). For both rice variety
groups, the AIC for the bottleneck plus sweeps model was
slightly lower than for the bottleneck plus migration models
(K ¼?2.26, indica; K ¼?3.28, japonica), but this difference is
likely not statistically meaningful given the various assump-
tions made. A separate (but not independent) assessment is
comparing the fit of the predictions of each model to the
data. The bottleneck plus sweeps model fits the marginal site-
frequency spectrum of indica quite well (GOF ¼ 13.86; p ¼
0.92), and does a slightly better job explaining the site-
frequency spectrum of tropical japonica than does the complex
demographic model incorporating bottlenecks plus migra-
tion (GOFsweeps þ bottleneck¼ 31.21, p ¼ 0.33; GOFbottlenecks þ
migration¼ 37.83; p ¼ 0.22). These results underscore the
importance of jointly modeling demographic and selective
effects when considering the evolution of domesticated crop
Domestication and the Shaping of Genome-Wide
Polymorphism Patterns in Rice
Population bottlenecks are believed to be the primary
demographic event associated with crop species origins, and
are the accepted mechanism to explain observed genome-
wide polymorphism levels among these taxa. There have been
concerted efforts to model the impact of population bottle-
necks on domesticated species genomes [27–29,42–44]. It
appears from our results, however, that a population bottle-
neck alone is inadequate to explain the observed nucleotide
polymorphism patterns in rice, one of the oldest and the most
predominant food crop species in the world.
A more complex demographic scenario involving very
strong bottlenecks that led to the fixation of alternate
alleles during the two rice domestication events, with
concurrent gene flow between variety groups, can explain
the site-frequency spectrum of indica and O. rufipogon.
However, this pure demography model requires a bottle-
neck 4-fold stronger in indica and twice as strong in tropical
japonica relative to the model that incorporates selection
(Figure 5; Table 2), and a relatively high migration rate
between domesticated rice and wild O. rufipogon popula-
tions. It is also important to note that the model is a poor fit
to the observed frequency distribution of alleles in tropical
Figure 5. Composite Likelihood Surfaces in indica and tropical japonica under Models Incorporating Selection
A density plot of the marginal composite log-likelihood surface of the parameters a and j, with the bottleneck severity t fixed to its estimate, under the
bottleneck plus sweeps model for (A) indica and (B) tropical japonica. The composite log-likelihood surface of the parameters a and j under the pure
selection model for (C) indica and (D) tropical japonica. The composite log-likelihood is represented as a deviation from the maximum log-likelihood,
with lighter values representing higher composite likelihoods. Numbers above (A) and (B) indicate the total number of sweeps in the rice genome
corresponding to each value of j, and numbers to the right of (B) and (D) represent the selection coefficient, s, corresponding to each value of a,
substituting an effective recombination rate of r ¼ 10?12and ln(2N) ¼ 10 into the expression: a ’ rs?1ln(2N), then solving for s.
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Polymorphism in Domesticated Rice
Domestication, however, is characterized by strong direc-
tional selection on a suite of traits that lead to the establish-
ment of cultivated species as distinct entities from their wild
progenitors within agricultural settings. We show that, in
contrast to the complex demographic model, a simple
bottleneck with sweeps model fits data from both tropical
japonica and indica well without requiring an extremely strong
domestication bottleneck. Since domesticated Asian rice has
been subject to artificial selection, the selection plus
demography model is a very plausible explanation for the
observed strong excess of high-frequency derived alleles in
domesticated rice varieties, and is consistent with recent
reports about domestication genes in rice [45,46].
Positive selection on specific genes results in reductions in
variation within a genome through selective sweeps [47,48].
Unlike bottlenecks, however, selection is thought to have
largely localized effects on genome variation. Our results
suggest that a model that incorporates selection can explain
patterns of nucleotide variation in a set of genome-wide
markers. We suggest two reasons why selective sweeps during
domestication could cause a genome-wide effect in O. sativa
and not in other cereal crop species such as maize. First, the
origin of domesticated Asian rice is associated with a
transition to self-fertilization, which results in a low effective
recombination rate and greatly increases the genomic
distance affected by selection. Second, O. sativa possesses
such a small genome (,400 Mb) that it is likely that a few
dozen to hundreds of selective sweeps could leave a genome-
Interestingly, under the bottleneck plus selective sweeps
model, the dynamics of domestication appear to differ in
significant ways between indica and tropical japonica. Despite
the fact that these two variety groups were domesticated from
the same species and both have contributed significantly to
Asian agriculture, it appears that the number of selective
events and/or the bottleneck severity differs between them. It
is possible that the two subspecies would diverge from each
other in the demographic patterns associated with domes-
tication, given that they were established by different
cultures. If this is correct, then tropical japonica appears to
have undergone a more severe bottleneck associated with
domestication. Alternatively, it may be that the establishment
of tropical japonica, which includes landraces that expanded to
upland growing areas, may be associated with stronger
selection pressures on a larger number of traits.
The process of domestication is one of recent, rapid species
evolution, and studies on the dynamics of this process inform
our understanding of the origins and diversification of new
species. Simple demographic scenarios that have been
employed in the past may not fully capture the domestication
process of some crop species such as Asian rice. Our models
indicate that selection and population bottlenecks together,
or more complex scenarios that invoke very strong bottle-
necks and current gene flow, could be responsible for
determining genome-wide variation in the rice genome, a
finding that has not been described in other domesticated
species. Domesticated crop species are particularly suitable
subjects in which to study the interaction between demo-
graphic events and selection in shaping species character-
istics, and exploring the relative contributions of these forces
require developing predictions for patterns of DNA poly-
morphism using models that allow selection to vary in timing
(i.e., both during and after population bottlenecks) and
strength. Nevertheless, our findings do underscore the
possible role that selection may play in shaping genomic
variation in domesticated species, reinforcing our apprecia-
tion of the foresight showed by Charles Darwin nearly a
century-and-a-half ago  when he sought to illustrate the
power of selection by drawing on the lessons learned from the
evolution of domesticated species.
Materials and Methods
Samples. A panel of 72 O. sativa accessions was chosen to represent
the diversity found within the species. These include representatives
of five major subpopulations identified in a previous study ,
including 21 indica, 18 tropical japonica, 21 temperate japonica, six aus, and
six aromatic accessions (Table S1). Most accessions are landraces, but
five accessions studied correspond to modern cultivars. Also included
in the panel were 21 accessions of the wild progenitor of rice, O.
rufipogon, along with one sample each of O. nivara (a close relative of O.
rufipogon not believed to have contributed to the ancestry of
cultivated rice) and the outgroup species O. barthii and O. meridionalis
DNA was extracted from single plants as described in  with
minor modifications. All O. sativa and one O. rufipogon accession
(International Rice Germplasm Collection [http://www.irri.org/grc/]
#105491) were self-fertilized for two generations prior to initiating
the study. Seeds from O. rufipogon from Nepal were collected in the
field by H. J. Koh and colleagues (Seoul National University); all other
seeds were obtained from germplasm repositories as summarized in
PCR and DNA sequencing. A total of 121 approximately 400–600
bp gene regions across the rice genome were chosen at random for
sequencing from a set of 6,591 ESTs . Four fragments were also
selected from genes coding for well-known allozymes, including:
catalase, acid phosphatase, pgi-a, and Adh. Primers were designed
from the Nipponbare genomic sequence available from Gramene
using Primer3 . Primers were designed in exons, and attempts
were made to include both exon and intron sequence within each
fragment. DNA sequencing was carried out in Genaissance’s
sequencing facilities (New Haven, Connecticut, United States) as
described in . Amplification and sequencing were successful for
111 fragments referred to as STS (Table S2). Approximately 54 kbp
per accession were sequenced, composed of, on average, 55% coding
and 45% noncoding sequence.
Base-pair calls, quality score assignment, and construction of
contigs were carried out using the Phred and Phrap programs (Codon
Code). Sequence alignment and editing were carried out with
BioLign Version 2.09.1 (Tom Hall, North Carolina State University,
Raleigh, North Carolina, United States). Heterozygous sites were
identified with Polyphred (Deborah Nickerson, University of Wash-
ington, Seattle, Washington, United States) and by visually inspecting
chromatograms for double peaks. Heterozygous sites were rare for O.
sativa. For heterozygous O. sativa and O. rufipogon sequences,
heterozygous sites were labeled with ambiguity codes. For all analyses,
the published sequence of Nipponbare was included.
To assess the sequencing error rate, 18 randomly chosen STS
fragments were resequenced in a single direction for four Oryza
accessions. Only three discordant base pairs within a single individual
in a single fragment sequence were observed. This corresponds to
three errors in 33,193 resequenced bp, or a sequencing error rate of
less than 0.01%.
Diversity analyses. Population structure among O. sativa and O.
rufipogon accessions was evaluated with STRUCTURE 2.1  using an
admixture model with no linkage. To limit the effect of correlation
between SNPs due to linkage, one SNP per fragment (the SNP with
the highest minor allele frequency across the entire accession set) was
used in the analysis. O. sativa is primarily selfing, and most accessions
exist as homozygotes; thus, SNP data were considered haploid for this
species. O. rufipogon is partially outcrossing, a condition that cannot
be adequately represented by considering each locus as diploid; thus,
SNP data for O. rufipogon were also considered haploid. Because
alternate alleles could occur at a given site in heterozygous O.
rufipogon accessions, ten datasets were created with randomly chosen
alternative base pairs in heterozygous individuals. Analyses were
carried out for all ten datasets. All analyses had a burn-in length of
50,000 iterations and a run length of 100,000 iterations. Three
replicates at each value of K (population number) were carried out.
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Polymorphism in Domesticated Rice
Simulations were run with uncorrelated allele frequencies. Results
were entirely consistent among replicate runs within datasets and
among datasets; the results from one run are presented in Figure 1
and Table S1.
To assess relationships among Oryza accessions, all STS fragment
alignments were concatenated to form a single dataset. Relationships
were estimated with a neighbor-joining analysis as implemented in
PAUP* version 4.0 b3 . Distances were calculated using the
Kimura two-parameter model. Branch bootstrap estimates were
obtained from 1,000 replicates.
Perl scripts were written to assess levels of nucleotide variation
(hW) and nucleotide diversity (hp) and Tajima’s D across rice groups
for all STS fragments, and to calculate the frequency distributions of
derived SNPs across the genome. For O. sativa accessions, where
heterozygotes were rare, all measures were calculated considering
each accession as contributing a single haplotype; for O. rufipogon
population measures, each accession was considered to contribute
two haplotypes, except for one accession (International Rice
Germplasm Collection [http://www.irri.org/grc/] #105491) from Ma-
laysia, which had been selfed for several generations prior to this
Analysis of the neutral bottleneck model. Under a neutral
bottleneck model, the history of rice domestication is represented
by recent population divergence, with one of the two daughter
populations experiencing a size bottleneck at divergence associated
with the founder effect at the time of domestication. We use the
sample frequencies of variable noncoding and synonymous nucleo-
tides in the STS alignments (i.e., the site-frequency spectrum of
putatively neutral SNPs) to infer the parameters of the bottleneck
model. Our analytical approach makes use of standard Wright-Fisher
population genetic theory within a Poisson random field setting [54–
57]. The assumptions of this model include independence among
SNPs, no selection, an underlying Poisson process governing
mutations, and a piecewise constant population of large size
amenable to modeling using diffusion approximations.
The model we employ is an extension of Williamson et al. ,
where we present the relevant population and statistical inference
theory for modeling a population experiencing a recent size change.
The key addition to our previous model is a second size change event,
corresponding to the post-bottleneck growth phase. This amounts to
modeling the components of the site-frequency spectrum (X1, X2, . . .,
Xn) as independent Poisson random variables with mean:
xið1 ? xÞn?ifðx;HÞdx
where h is the genome-wide mutation rate, x represents the
(unknown) population frequencies of mutations, and f(x;H) is the
distribution of mutation frequencies given demographic history
parameters H ¼ fm,s1,s2g. These parameters are: the time back until
the start of domestication (s1), duration of the bottleneck (s2), ratio of
current population to ancestral population size (m2), and relative size
of the bottleneck population to the ancestral population (mb). The
duration of the bottleneck was assumed to be 25% of the time back
until domestication (s2 ¼ 0.25 3 s1), which is consistent with
archaeological data suggesting domestication took 3,000 y and began
12,000 y ago. The mutation rate, h, was estimated from the number of
synonymous and noncoding segregating SNPs assuming O. rufipogon
represented a population of constant size. This assumption is quite
reasonable given the excellent concordance between the O. rufipogon
and the predictions of the standard neutral model (Figure 4), and is
equivalent to using Watterson’s (1975) estimator of h. In order to
account for missing data, we fitted the population bottleneck model
using the projected site-frequency spectrum for a sample of n ¼ 16
Alternative demographic scenarios for rice domestication. We
considered alternative demographic scenarios, in which ancestral
population subdivision, followed by gene flow between rufipogon,
indica, and tropical japonica, led to an excess of high-frequency derived
alleles in domesticated rice groups, as well as a simpler model that has
no ancestral substructure. For these models, the composite likelihood
function was based on the marginal site-frequency spectrum of each
of the three groups analyzed. For ease of notation, let Sind, Sjap, and
Srufbe the number of SNPs for which we could distinguish ancestral
from derived alleles using the outgroup (223, 172, and 636,
respectively). Let y denote the set of derived allele counts for each
SNP, with y?ind, y?jap, and y?rufreferring to set of SNPs for indica, tropical
japonica, and O. rufipogon (with lengths Sind, Sjap, and Sruf, respectively).
To account for missing data, let n refer to the number of
chromosomes sequenced at each SNP, with n?ind, n?jap, and n?rufthe
vector for each group (again with lengths Sind, Sjap, and Sruf,
respectively). For a given demographic model discussed above (the
parameters of which we collectively denote H), the composite
likelihood function is written as
LðyjHÞ ¼ fPrðSindjHÞ
where Pr(S?jH) is assumed to follow a Poisson probability of
observing S? SNPs in a given population under the demographic
model H assuming the population scaled mutation rate h ¼ 148.6
(estimated using the observed number of SNPs in O. rufipogon), and
Prðy:;n:jHÞ is the probability of observing a SNP configuration in a
given population under the demographic model. It is important to
note that the inference scheme assumes the allele frequency
distributions, conditional on the observed number of segregating
sites and demographic parameters, are independent among popula-
tions. This composite-likelihood function (like all composite-like-
lihood functions) must, therefore, be taken as an approximation of
the true likelihood function since it ignores dependencies among
SNPs due to linkage and among populations due to shared variation.
To account for missing data at an arbitrary SNP k in population x, we
if no missing
where Pz(H,Nx) is the expected proportion of SNPs at a frequency z in
a sample of Nxchromosomes under the demographic model H, and
the fraction within the summation represents the hypergeometric
probability of sampling yx
chromosomes if the unknown frequency of the SNP were j out of Nx
(summed over all possible underlying SNP frequencies, j). Details on
calculating the expected number of SNPs in each population as well
as Pz(H,Nx) are described below.
Optimizing complex neutral demographic models. For a given set
of parameters, H, we determine the expected site-frequency spectra
for all three populations (O. rufipogon, indica, and tropical japonica) using
100,000 iterations of the coalescent simulation program ms 
conditional on the observed genome-wide estimate of h for O.
rufipogon. To generate data under this model, we used the following
ms 80 200000 –t 148.6487 –r 148.6487 111 –I 3 21 18 41 M
–en 0.5*0.75*s11 mB–en 0.5*0.75*s12mB–ej 0.5*s11 3 –ej s12 3 ?em
0.5*s13 1 0 –em 0.5*s13 2 0 ?n 1 mI–n 2 mJ.
Note that the factor 0.75 enters from the assumption that the
bottleneck lasted 3,000 y of the 12,000 y time since domestication
began, and 0.5 enters since ms scales time in units of 4N generations.
To optimize the three- and five-dimensional likelihood surface, we
used an iterative technique, whereby a very coarse grid is initially
chosen for each parameter, followed by successively tighter intervals
containing the previous iteration’s maximum likelihood estimates.
Because we were pooling data across 111 STS loci, we generated our
expected site-frequency spectrum accordingly. Although recombina-
tion within or between STS loci will not affect the expected number
of segregating sites or the expected site frequency spectrum under a
neutral demographic model, it does impact the rate at which
simulations will approach them. We therefore assumed 111 mostly
independent loci of equal size when generating our expectations.
Modified Pearson Goodness-of-Fit test. In order to compare the fit
of the demographic model to the observed data accounting for
missing genotypes and partial selfing, we considered a projection of
the observed and predicted site-frequency spectra into a sample of
size n¼16 chromosomes from each of the three populations using the
hypergeometric distribution. The ‘‘observed’’ data can be thought of
as the predicted SFS in a subsample of n¼16 based on the actual SNP
data assuming each of the O. sativa accessions contributes one
chromosome to the observed allele frequency spectrum, and each of
kderived alleles in a subsample of nx
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Polymorphism in Domesticated Rice
the O. rufipogon accessions contributes two, with the exception of one
accession that was known to have been purified. The ‘‘expected’’ data
are the predicted marginal site-frequency spectrum at the maximum
composite-likelihood estimates of the parameters from the complex
demographic model that includes bottlenecks in the two domes-
ticated populations, migration within domesticated populations, and
migration between domesticated and ancestral populations. There
were 45 observed data points (15 segregating site-frequency spectrum
components multiplied by three populations), and the GOF statistic
for a given population was tabulated as GOF ¼P15
containing 111 independent loci with no recombination within loci
under the best-fitting demographic model. For each dataset, we then
calculated the GOF test statistic using the expected site-frequency
spectrum from Figure 4 scaled to the observed number of segregating
sites within each of the subpopulations. Ideally, one would re-
estimate the demographic parameters in order to fully mimic the
inference procedure we used. Unfortunately, estimation of the
demographic parameters was extremely computationally intensive
for each dataset; the single observed STS data point analyzed here,
for example, took over a week of computer time on a dedicated 100-
node computing cluster.
Composite likelihood under multiple sweeps models. Conditioning
on the observed number of segregating sites in the dataset, the site-
frequency spectrum is multinomially distributed with frequency
probabilities according to Equation 1. For the pure selection model,
the composite likelihood is:
where qris the normalized site-frequency spectrum of O. rufipogon.
For the bottleneck plus multiple sweeps model, the composite
where qmis the predicted spectrum from a neutral bottleneck model
with severity m. Equations 5 and 6 can be maximized to quantify the
number and strength of selective sweeps in domestic rice, and the
optimization of Equation 5 provides an estimate of the severity of the
population bottleneck that preceded the selective sweep.
The background site-frequency spectrum for the bottleneck plus
multiple sweeps model. The bottleneck plus sweeps model assumes
that a short bottleneck (representing to the founding of domestic
populations) precedes the selective sweeps. To calculate the back-
ground site-frequency spectrum at the end of the bottleneck and the
beginning of the selective sweeps, we again used numerical methods
to solve the one-population diffusion equation with population size
order to assign a p-value, we simulated 10,000 datasets each
qð1 ? qÞ
In this case, the recovery time, s1, was set to 0, corresponding to the
assumption that new mutations since the bottleneck do not make a
strong contribution to the observed SFS. Because the bottleneck
duration, s2, and the severity, m, are confounded parameters, we set s2
¼ 0.01 and allow m to vary. With f(q,s2) as the numerical solution to
Equation 7 evaluated at time s2, we calculate the background site-
frequency spectrum qm as:
qið1 ? qÞn?ifðq;s2Þdq
AIC as a test statistic for comparing non-nested models. To
properly interpret differences in AIC between models, we simulated
10,000 datasets of 111 nonrecombining loci under the null hypothesis
of the best-fitting neutral bottleneck model using the ms coalescent
simulation program . Because we did not allow recombination
within loci, these simulations conservatively account for the effects of
linkage. For each simulated dataset, we found the maximum
composite likelihoods under each model (bottleneck, bottleneck plus
migration, multiple sweeps, and bottleneck plus sweeps) and
calculated the AIC value. The AIC statistic of model i is defined as:
AICi¼?2(lmaxi? ki) where lmaxiis the maximum likelihood under
model i and kiis the number of free parameters in model i. We used K
¼ AIC1? AIC2as a test statistic for comparing the bottleneck and
alternative models using a one-tailed test: the p-value was estimated
as the proportion of simulations under the null distribution with K .
Figure S1. Clustering of Oryza Accessions Based on Neighbor-Joining
Analysis of Concatenated STS Sequences
Numbers by branches are bootstraps of 1,000 replicates. Only
branches with a bootstrap value higher than 60% for major clades
(five or more accessions) are labeled. The monophyly of each rice
variety group is well supported, with the exception of tropical japonica.
The accession M202-new is an elite temperate japonica line that has
been subjected to possible crosses with other groups, perhaps
explaining its inclusion within the tropical japonica.
Found at doi:10.1371/journal.pgen.0030163.sg001 (409 KB EPS).
Figure S2. Frequency Distribution of Tajima’s D Values for All STS
Sampled in (A) indica, (B) tropical japonica, and (C) O. rufipogon
Found at doi:10.1371/journal.pgen.0030163.sg002 (373 KB EPS).
Figure S3. The Distribution of Allele Frequency in O. rufipogon for
Derived Alleles That Are at High Frequency in indica or tropical
Notably, most alleles are at low to intermediate frequency in O.
rufipogon, consistent with multiple selective sweeps in O. sativa, and
discounting the possibility of misidentification of ancestral alleles or
interspecific introgression being responsible for the pattern observed
in rice. HFD, high-frequency derived SNPs.
Found at doi:10.1371/journal.pgen.0030163.sg003 (390 KB EPS).
Figure S4. The Genomic Distribution of STS Fragments Contributing
High-Frequency Derived SNPs in indica and tropical japonica
In each group, high-frequency derived SNPs occur in ten of 12 rice
chromosomes. Fragments containing high-frequency derived SNPs
comprise a large portion of fragments containing any variation at all
in each O. sativa group. In both rice groups, the sample of STS
fragments used to construct the site-frequency spectrum is slightly
lower than 111 due to missing data in O. meridionalis.
Found at doi:10.1371/journal.pgen.0030163.sg004 (433 KB EPS).
Table S1. Oryza Accessions Used in the Study and Inferred Ancestry
Found at doi:10.1371/journal.pgen.0030163.st001 (45 KB XLS).
Table S2. STS Fragment Information and Silent Sites Diversity
Measures for the Various Oryza Groups
Found at doi:10.1371/journal.pgen.0030163.st002 (133 KB XLS).
The National Center for Biotechnology Information GenBank (http://
www.ncbi.nlm.nih.gov/Genbank) ID numbers for the sequences and
alignments discussed in this article are EF000002–EF010509.
We are grateful to two anonymous reviewers for suggestions that
much improved the manuscript.
Author contributions. RN, SRM, CDB, and MDP conceived the
experiments. ALC, KMO, and MDP designed the experiments. ALC
collected the data. ALC, SHW, RDH, and CDB analyzed the data. AB,
AFA, NRP, TLY, and SRM and contributed materials/analysis tools.
ALC, SHW, CDB, and MDP wrote the paper.
Funding. This work was funded by the US National Science
Foundation Plant Genome Research Program..
Competing interests. The authors have declared that no competing
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Polymorphism in Domesticated Rice
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PLoS Genetics | www.plosgenetics.org September 2007 | Volume 3 | Issue 9 | e1631756
Polymorphism in Domesticated Rice