Gu, Z. et al. Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 102, 1092-1097

Article (PDF Available)inProceedings of the National Academy of Sciences 102(4):1092-7 · February 2005with37 Reads
DOI: 10.1073/pnas.0409159102 · Source: PubMed
Abstract
By using the maximum likelihood method, we made a genome-wide comparison of the evolutionary rates in the lineages leading to the laboratory strain (S288c) and a wild strain (YJM789) of Saccharomyces cerevisiae and found that genes in the laboratory strain tend to evolve faster than in the wild strain. The pattern of elevated evolution suggests that relaxation of selection intensity is the dominant underlying reason, which is consistent with recurrent bottlenecks in the S. cerevisiae laboratory strain population. Supporting this conclusion are the following observations: (i) the increases in nonsynonymous evolutionary rate occur for genes in all functional categories; (ii) most of the synonymous evolutionary rate increases in S288c occur in genes with strong codon usage bias; (iii) genes under stronger negative selection have a larger increase in nonsynonymous evolutionary rate; and (iv) more genes with adaptive evolution were detected in the laboratory strain, but they do not account for the majority of the increased evolution. The present discoveries suggest that experimental and possible industrial manipulations of the laboratory strain of yeast could have had a strong effect on the genetic makeup of this model organism. Furthermore, they imply an evolution of laboratory model organisms away from their wild counterparts, questioning the relevancy of the models especially when extensive laboratory cultivation has occurred. In addition, these results shed light on the evolution of livestock and crop species that have been under human domestication for years.

Figures

Elevated evolutionary rates in the laboratory strain
of
Saccharomyces cerevisiae
Zhenglong Gu*
†‡
, Lior David*
, Dmitri Petrov
§
, Ted Jones*, Ronald W. Davis*
, and Lars M. Steinmetz*
‡¶
*Stanford Genome Technology Center, 855 California Avenue, Palo Alto, CA 94304;
Department of Biochemistry, Stanford University School of Medicine,
Stanford, CA 94305;
§
Department of Biological Sciences, Stanford University, Stanford, CA 94305; and
European Molecular Biology Laboratory,
Meyerhofstrasse 1, 69117 Heidelberg, Germany
Communicated by Wen-Hsiung Li, University of Chicago, Chicago, IL, December 8, 2004 (received for review October 4, 2004)
By using the maximum likelihood method, we made a genome-
wide comparison of the evolutionary rates in the lineages leading
to the laboratory strain (S288c) and a wild strain (YJM789) of
Saccharomyces cerevisiae and found that genes in the laboratory
strain tend to evolve faster than in the wild strain. The pattern of
elevated evolution suggests that relaxation of selection intensity
is the dominant underlying reason, which is consistent with recur-
rent bottlenecks in the S. cerevisiae laboratory strain population.
Supporting this conclusion are the following observations: (i) the
increases in nonsynonymous evolutionary rate occur for genes in
all functional categories; (ii) most of the synonymous evolutionary
rate increases in S288c occur in genes with strong codon usage bias;
(iii) genes under stronger negative selection have a larger increase
in nonsynonymous evolutionary rate; and (iv) more genes with
adaptive evolution were detected in the laboratory strain, but they
do not account for the majority of the increased evolution. The
present discoveries suggest that experimental and possible indus-
trial manipulations of the laboratory strain of yeast could have had
a strong effect on the genetic makeup of this model organism.
Furthermore, they imply an evolution of laboratory model organ-
isms away from their wild counterparts, questioning the relevancy
of the models especially when extensive laboratory cultivation has
occurred. In addition, these results shed light on the evolution of
livestock and crop species that have been under human domesti-
cation for years.
model organism slightly deleterious mutation yeast evolution
T
he most c ommonly used Saccharomyces cerevisiae haploid in
the laboratory, S288c, for which the whole genome sequence
is k nown (1), has 88% of its genome derived f rom a strain
(EM93) isolated from a rotten fig 70 years ago (2). The origin
of EM93 before fig isolation is unclear. It could be a natural fig
isolate or, rather, a c ontaminant derived from an industrial strain
(2). The domestication of S. cerevisiae therefore can be dated
back to somewhere bet ween 70 and several hundred years ago.
Because of the short generation time of yeast, the experimental
practices in the past several decades and the possible industrial
man ipulations could have lef t significant footprints on the
evolution of the S288c strain. These activities can lead to peculiar
evolutionary trajectories because frequent passages of the strains
through severe bottlenecks, which may even reduce populations
down to a single cell on ac count of common experimental
practices, can result in a significant reduction in the effective
population size and thus to fixation of mutations that would be
too deleterious to become fixed under natural conditions. This
process occurs because population genetics theory predicts that
mut ations with s 12N
e
, where s is the selection coefficient
and N
e
is the effective population size, behave nearly neutrally
(3–8). Indeed, increased evolutionary rates of individual genes
due to population size reduction were rec orded for diverse
organ isms such as endosymbiotic bacteria and island birds (9,
10). Further more, in some cases more targeted evolutionary
changes can occur as laboratory strains experience a loss of
specific environmental selection pressure or adapt to the labo-
ratory growth conditions. Specific laboratory adaptation for
various organisms is described in refs. 11 and 12.
If such evolution did occur and for med a significant propor-
tion of the evolutionary changes in the history leading to the
laboratory strain, we would expect to see an accelerated evolu-
tion in this lineage. If relaxation of selection due to population
size reduction is the most dominant factor, the increase in
evolutionary rate should not be centralized on genes with
specific function, because the changes of population structure
should affect all genes under selection. Furthermore, this hy-
pothesis would predict that genes under different selection
pressure have different changes in evolutionary rate as the
ef fective population size reduces. Conversely, increases in evo-
lutionary rate due to adaptive evolution or relaxation of selection
caused by loss of particular environmental selection pressure
should only occur for some genes, those that are functionally
relevant to the specific change. In this study, we tested these
hypotheses by comparing the evolutionary rates (synonymous,
nonsynony mous, and the ratio of the two) in the lineages to the
laboratory strain (S288c) and a wild strain (YJM789) that was
isolated from the lung of an AIDS patient (13).
Shotgun sequencing of the YJM789 genome (L.M.S., T.J.,
L.D., M. Miranda, D. Bruno, C. Komp, M. Nguyen, R. Tamse,
J. Wilhelmy, R.W. Hyman, and R.W.D., unpublished dat a)
shows an average difference to S288c of (9.8 0.2) 10
3
changes per synonymous site. YJM789 is a good candidate to
c ompare with S288c, because it is not too divergent from the
laboratory strain: The evolutionary changes accumulated be-
cause of laboratory and possible industrial manipulations there-
fore can constitute a significant part of the evolution between
these two strains. Although the short separation time between
the strains makes it statistically dif ficult to see the noteworthy
ef fects of evolutionary forces, such as population-size reduction,
on individual genes, the sequencing of the whole genome of
YJM789 prov ides an opportunity to analyze evolutionary
changes globally. By combining all genes in the genome, we can
detect traces left by different evolutionary forces even if they
have acted for a short time.
The genome sequence of Saccharomyces paradox us, the closest
sequenced species to S. cerevisiae (14), was used as an outg roup
in a phylogenetic analysis. Altogether, 4,020 genes with good
alignment among the three organisms were analyzed. As pre-
dicted from the evolution of strains that experience passage
through recurrent bottlenecks, a significantly higher evolution-
ary rate, at both the synonymous and nonsynony mous sites, was
detected in the lineage to S288c than to YJM789, and the
increase of nonsynonymous evolutionary rate was shown to
oc cur for genes in all functional categories. By dividing genes
Abbreviation: ENC, effective number of codons.
Data deposition: The sequence reported in this paper has been deposited in the GenBank
database (accession no. AAFW00000000).
To whom correspondence may be sent at the (Z.G.) and (L.M.S.) addresses. E-mail:
zgu@stanford.edu or larsms@embl.de.
© 2005 by The National Academy of Sciences of the USA
1092–1097
PNAS
January 25, 2005
vol. 102
no. 4 www.pnas.orgcgidoi10.1073pnas.0409159102
into different groups based on their codon usage bias, we
demonstrate that the increase of evolutionary rate at synony-
mous sites occurs mostly on genes with strong codon usage bias,
whereas the increase of nonsynony mous evolutionary rate is
higher for genes under stronger negative selection. Furthermore,
adaptive evolution was detected for more genes in the laboratory
strain than in YJM789; however, the faster evolution in the
laboratory strain still exists even after excluding genes under
positive selection. This finding implies that adaptive evolution is
not the major reason for the observed evolutionary rate increase
in the laboratory strain.
Materials and Methods
Genomic Sequences and Analysis. The genome of S. cerevisiae strain
YJM789 was sequenced by the Stanford Genome Technology
Center. Completion of the genome is in progress (L.M.S., T.J.,
L.D., M. Miranda, D. Bruno, C. Komp, M. Nguyen, R. Tamse,
J. Wilhelmy, R. W. Hy man, and R.W.D. unpublished data).
From the shotgun assembly (Version 2, www-sequence.stan-
ford.edu) only contigs with 10 synteny-defined orthologous
genes between S288c and YJM789 were included in this study.
The genome sequence of S. paradoxus was used as the outgroup
in a phylogenetic analysis (Fig. 1). Orthologous genes between
S. cerevisiae (S288c) and S. paradoxus were defined by Kellis et
al . (14) (www.broad.mit.eduannotationfungic omp yeasts
downloads.html). The
CLUST ALW alignments of the three-way
orthologous proteins were verified individually by eye. Alto-
gether 4,020 genes were included in the analysis. Coding DNA
sequences were aligned based on the protein alignments.
A nalysis of the evolutionary changes in each lineage was
performed by using
C ODEML in the PAML package (15, 16). The
f ree ratio model was used in estimating the synonymous and
nonsynony mous changes in each branch. Branch-Site Models
(17) were used in detecting genes with positive evolution (see
Results). Codon usage bias for each gene was estimated by using
C ODONW (www.molbiol.ox.ac.ukcu). For a gene, the smaller the
ef fective number of c odons (ENC), the stronger the codon usage
bias (18). The codon preference for each amino acid was defined
as in ref. 19.
To c ompare evolutionary rates in two branches for genes with
dif ferent functions, we grouped genes based on the Gene
Ontology system (www.geneontology.org). Within each cate-
gory, evolutionary changes for individual genes were added
together to estimate evolutionary rates for synonymous (K
S
) and
nonsynony mous (K
A
) sites. The variance of the evolutionary rate
ratios (or differences) bet ween S288c and YJM789 were esti-
mated by a bootstrap procedure (20). If there are N genes in one
category, the same number of genes was sampled with replace-
ment within the category, and the ratio (or difference) of
evolutionary rate was calculated. The variance was estimated by
repeating the sampling 100 times. Student’s t test was used in
assessing whether the ratio of evolutionary rate between S288c
and YJM789 was significantly larger than 1 (or 0 for the
evolutionary rate difference).
To deter mine the evolutionary rate changes for genes under
dif ferent selection pressures, we grouped the studied genes into
categories based on their c odon usage bias. The stronger the
c odon usage bias, the higher the negative selection pressure on
a gene. This assumption is valid because evolutionary rates at
nonsynony mous or synonymous sites or the ratio of the two are
negatively related with gene codon usage bias (21–25). To
estimate the mean and variance of the evolutionary rate change
bet ween S288c and YJM789 within each ENC category, the
same analysis described above for categories of gene function
was performed. We report the results based on codon usage bias
in S288c, but the same conclusions were reached when codon
usage f rom orthologous genes in YJM789 or the average of
S288c and YJM789 were used in the analysis. The number of
categories also did not af fect the conclusions (data not shown).
Excluding Genes from Different Genetic Backgrounds. Winzeler et al.
(26) compared coding regions of S288c and EM93 by using
Af fymetrix microarrays, and polymorphisms were identified
bet ween these t wo strains. As performed by these authors, we
clustered all polymorphic probes within 30-kb intervals and
extended the boundaries of each cluster 10 kb to either side.
Clusters with fewer than three polymorphic probes were dis-
missed. Genes located in these clusters (16%) were regarded
as genes in highly polymorphic regions between S288c and
EM93. Because it was estimated that 12% of the S288c
genomes is derived f rom genetic backgrounds other than EM93
(2), to be conservative we excluded all of the genes in these highly
poly morphic regions. The same analyses as those for the whole
genome were carried out for the remaining genes.
Results
Increased Evolutionary Rates in the Lineage to the Laboratory Strain
(S288c). The maximum likelihood method was used to estimate
the evolutionary changes in each branch. R, the evolutionary rate
measured by the ratio of nonsynonymous (K
A
) over synonymous
(K
S
) evolutionary rates, was calculated (Fig. 1). We found that,
as has been shown in other studies (27–32), R is larger for
poly morphism than for divergence between species. For exam-
ple, R is 2-fold larger in the S288 and YJM789 branches than
in the S. paradoxus branch (Table 1). The salient discovery for
this comparison, however, is that at the genome level R is
sign ificantly larger in the lineage to S288c than to YJM789. As
shown in Table 1, when the evolutionary changes are added up
for all studied genes, 21% (4400.53631.4 1.21) more non-
synony mous changes were detected in the S288c branch than in
the YJM789 branch. Even after normalizing the nonsynonymous
dif ference by the synonymous difference, a 15% (0.201
0.174 1.155) increase in the laboratory strain was detected.
The dif ference is st atistically significant by Fisher’s exact test
(P 0.001). When the same analyses were performed separately
on experimentally verified and unverified genes, similar patterns
were observed (Table 5, which is published as supporting
infor mation on the PNAS web site).
Previous study showed that 88% of the S288c genome was
derived from a strain called EM93, whereas the rest of the
genome originated from a mixture of other genetic backgrounds
(2). Genes derived from strains other than EM93 might interfere
with identif ying the real evolutionary changes in the lineage to
the laboratory strain. To eliminate this effect, we excluded genes
located in highly polymorphic regions between S288c and EM93.
As shown in Table 1, the difference in evolutionary rates
bet ween the two lineages based on the remaining 3,357 genes
Fig. 1. Phylogenetic relationship between the two studied S. cerevisiae
strains (S288c and YJM789) and the outgroup of S. paradoxus. The arrow
indicates an approximate time when EM93, an ancestor of S288c, was isolated
from a rotten fig (2). The time of the most recent common ancestor of EM93
and YJM789 could not be reliably estimated.
Gu et al. PNAS
January 25, 2005
vol. 102
no. 4
1093
EVOLUTION
remains statistically significant. To exclude possible effects
c oming from different genetic backgrounds, we only used genes
located outside of the highly polymorphic regions between S288c
and EM93 in the following analyses.
Increased Evolutionary Rates Found for Genes in All Functional Cat-
egories.
We investigated possible reasons for the evolutionary
rate increase in the laboratory strain. If population-size reduc-
tion is the major underlying reason, the evolutionary rate should
increase for all genes that experience negative selection regard-
less of their function. To test this prediction, the Gene Ontology
system was used to g roup genes into different functional cate-
gories (33). We then compared the evolutionary rate in the S288c
and YJM789 branches within each functional category. As
shown in Fig. 2 and Fig. 5, which is published as supporting
infor mation on the PNAS web site, an increased evolutionary
rate (R) in the laboratory strain was observed for all nine
functional categories. The level of increase, however, was not
identical for each group. For example, genes involved in tran-
scriptional activity had the highest increase in evolutionary rate
in the laboratory strain.
Greater Increase in Evolutionary Rates for Genes Under Stronger
Negative Selection.
To determine whether the evolutionary rate
increase varies for genes with different selection pressure we
grouped genes into different categories based on their codon
usage bias (ENC). Indeed, evolutionary rates at nonsynonymous
or synonymous sites or the ratio of the two have been shown to
be negatively related with gene codon usage bias (21–25).
Therefore, the more the codon usage bias for a gene, the stronger
the negative selection pressure for that gene.
Table 2 lists the number of increased evolutionary changes in
S288c for each codon usage bias category. Of the increased
synony mous changes in S228c, 76.3% (230.7 of 302.2) occurred
in the first two categories (with strongest codon usage bias, P
0.001 for enrichment). This result cannot be ex plained by a
mut ation rate increase at the whole genome level or by more
generations in the lineage to the laboratory strain, both of which
would cause a uniform increase in K
S
for all g roups. Conversely,
population size reduction can cause this pattern because the
synony mous sites for genes with strong codon usage bias are
under negative selection. With decreasing population size, the
selective pressure at the synonymous sites of these genes will be
relaxed, and the evolutionary rate will increase.
As shown in Table 2, the nonsynonymous evolutionary rate
increase in S288c is also enriched in genes with strong codon
usage bias [e.g., 46.4% (267.5 576.7) of increased nonsynony-
mous changes in S228c occurred in the first two categories; P
0.001 for enrichment]. When R (K
A
K
S
) was investigated, we
observed the same pattern, namely that the increased evolution-
ary rate in the laboratory strain is highest for genes with the
strongest negative selection and decreases as selection intensity
on the genes, reflected here by the gene codon usage bias,
decreases (Fig. 3). The same trend also was observed when the
dif ference instead of the ratio of the evolutionary rate between
the S288c and YJM789 branches was investigated (Fig. 3 Inset).
Further more, gene groupings based on protein dispensability or
R between the S288cYJM789 ancestor and S. paradox us, in-
stead of ENC, led to similar conclusions (data not shown).
Interestingly, as population size reduces, relatively more dele-
terious mutations are expected to become nearly neutral for
genes under stronger negative selection (Fig. 6, which is pub-
lished as supporting information on the PNAS web site), which
is consistent with the above observations.
Table 1. Number of synonymous and nonsynonymous changes in the lineages to S288c,
YJM789, and S. paradoxus
Strain
All genes Genes in low polymorphic regions
S* N* R K
A
K
S
* SNR K
A
K
S
S. paradoxus 625,466.5 169,826.8 0.104 523,254.7 142,368.5 0.104
S288c 8,342.3 4,400.5 0.201 6,844.6 3,610.3 0.201
YJM789 7,956.1 3,631.4 0.174 6,542.4 3,033.6 0.177
S288cYJM789 1.05 1.21 1.16 1.05 1.19 1.14
In the left part of the table 4,020 genes were analyzed; in the right part 663 genes that locate in the highly
polymorphic regions between S288c and EM93 were excluded. Fisher’s exact test shows that the nonsynonymous
evolutionary rate is significantly higher in S288c than in YJM789 for both groups of genes.
*S and N represent the number of synonymous and nonsynonymous changes, respectively. K
S
and K
A
represent
the number of synonymous and nonsynonymous changes per synonymous and nonsynonymous site,
respectively.
Fig. 2. Relative increase of evolutionary rate in the laboratory strain for
genes in different functional categories. The groups were ordered by decreas-
ing number of genes in each category. The x-axis represents the ratio of
evolutionary rate (R K
A
/K
S
) in S288c to that in YJM789 (see Fig. 5 for the
absolute increase in evolutionary rates in each functional category).
***
, P
0.001 by Student’s t test for ratio 1. Genes in highly polymorphic regions
between S288c and EM93 were excluded.
Table 2. Increase of evolutionary changes for genes with
different codon usage in the lineage to S288c
Codon usage bias categories
123456
Synonymous 83.9 146.8 53.9 6.2 29.4 5.6
Nonsynonymous 103.8 163.7 110.3 100.8 63.1 35
Categories were defined as in Fig. 3, shown in order of decreasing codon
usage bias. The numbers are the difference in evolutionary changes between
S288c and YJM789 branches (S288c YJM789).
1094
www.pnas.orgcgidoi10.1073pnas.0409159102 Gu et al.
Adaptive Evolution Is Not the Major Reason for the Observed Evolu-
tionary Rate Increase in the Laboratory Strain.
Adaptive evolution of
S288c to the laboratory growth conditions also can be a candi-
date reason for the observed increase in evolutionary rate in this
strain. To examine this possibility, we applied a maximum
likelihood method for identif ying genes with positive selection at
the codon level from both lineages (18). Two hypotheses were
c ompared for either lineage by using the likelihood ratio test: the
null hypothesis assuming neutral (K
A
K
S
1orK
A
K
S
1)
evolution for each codon site and the alternative hypothesis that
allows some sites to evolve with K
A
K
S
. Those genes with
sign ificantly higher likelihood for the alternative hypothesis were
regarded as genes under positive selection.
Table 3 lists the number of genes with evidence of adaptation
under various st atistical significance levels in either lineage.
A lthough we always observed more genes w ith adaptive evolu-
tion in the lineage to S288c than to YJM789, we argue that
adaptive evolution is not the major reason for the evolutionary
rate increase in the laboratory strain for two reasons: First, we
did not see more genes with evidence of adaptation than
ex pected by random chance. For example, under P 0.05, 138
genes with positive signals were detected in S288c, whereas we
ex pected to see 4,020 0.05 201 genes to pass this test by
random chance. Sec ond, the evolutionary rate dif ference be-
t ween the t wo lineages was still highly significant even after
excluding those genes with adaptive evolution; in the latter
analysis the evolutionary rate in the S288c branch still st ays
14% higher for the remaining genes (Table 6, which is pub-
lished as supporting information on the PNAS web site).
Discussion
Evolutionary rate (R) appears 15% faster in the laboratory
strain S288c of yeast than in the wild strain YJM789. If this
increase occurred because of laboratory and possible industrial
man ipulations, the actual rate of evolution in S288c during that
period may be much higher because the observed results are
averaged across the whole branch after the separation of S288c
and YJM789 from their common ancestor. Several reasons, such
as increased mutation rate, more generations, relaxation of
Fig. 4. Distribution of genes with adaptive evolution in each functional
category for the lineages to S288c and YJM789.
*
, P 0.05 by Fisher’s exact
test.
Fig. 3. Increase of evolutionary rate in the laboratory strain for genes under different negative selection. The genes were divided into six categories basedon
their ranked codon usage bias. Groups are in order of decreasing codon usage bias (increasing ENC). Each group has 559 genes (except group 6, which has 562
genes). (Inset) The absolute evolutionary rate increase in the laboratory strain. The dashed line represents the linear regression line. Grouping genes based on
the average codon usage between S288c and YJM789 gave similar results (data not shown).
***
, P 0.001 by Student’s t test for ratio 1. Genes in highly
polymorphic regions between S288c and EM93 were excluded.
Table 3. Number of genes with adaptive evolution in the S288c
and YJM789 branches
Threshold
P value S288c YJM789 Ratio
0.05 138 (112) 93 (76) 1.48 (1.47)
0.01 65 (54) 42 (32) 1.55 (1.69)
0.001 23 (21) 16 (11) 1.44 (1.91)
The values in parentheses are after excluding genes in highly polymorphic
regions between S288c and EM93.
Gu et al. PNAS
January 25, 2005
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no. 4
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EVOLUTION
selection pressure, and adaptive evolution in the laboratory
lineage, can lead to elevated evolutionary rates (34, 35). The first
t wo reasons, i.e., increased mutation rate and more generations,
cannot be the major underlying reasons because the evolutionary
rate difference observed above for amino acid change was
nor malized by synony mous change. Furthermore, as shown in
Table 2, the slight increase in synonymous change in S288c
oc curs mostly on genes with strong codon usage bias, which is
c onsistent w ith expectation from fixation of slightly deleterious
mut ations due to population size reduction.
A decrease in selection coefficients (s) also will lead to a
relaxation of selection pressure. The evolutionary rate increase was
observed for genes in all functional categories, which implie s
relaxation of selection due to reduction in population size (N
e
)
rather than selection coefficients (s), because the latter will likely
occur on genes with specific functions. For the same reason we
believe that adaptive evolution is not the major mechanism under-
lying the evolutionary rate increase in the laboratory strain. In
addition, if all (or most) of the increased evolutionary rate in the
laboratory strain were due to adaptive evolution, S288c should be
more fit under laboratory growth conditions than YJM789. The
data are not consistent with this expectation: YJM789 grows faster
than S288c under laboratory growth conditions (36).
Nevertheless, genes showing adaptive evolution in the labo-
ratory strain can provide immediate, biologically meaningful
hypotheses for further investigation. For example, YBR203W
(COS111), a gene involved in the response to antifungal drugs
(37), shows significant positive selection in the laboratory strain
(P 0.001 by likelihood ratio test). Furthermore, it will be
interesting to investigate the functional consequences of the
adapt ation detected in genes involved in transcription, 14 of
which show adaptive evolution in S288c, whereas this number is
only 3 in YJM789 (Fig. 4, P 0.05 by Fisher’s exact test; see
Tables 7 and 8, which are published as supporting information
on the PNAS web site, for the list of all genes w ith adaptive
evolution in either lineage).
Increased evolutionary rates for individual genes as a result of
population size reduction have been reported in various organ-
isms (9, 10, 38). Several studies showed that elevated evolution-
ary rates are usually accompanied by relaxation of codon usage
bias (9, 38). To see whether this is the case in our dat a, we further
analyzed the direction of synonymous change in either lineage.
More changes from preferred to unpreferred codons would be
ex pected in S288c if a relaxation of codon usage bias occurred.
As shown in Table 4, in the laboratory strain we observed a
marginally higher rate of synonymous change from preferred to
unpreferred c odons for genes with strong codon usage bias. The
reverse direction of synonymous change (unpreferred to pre-
ferred) is not significantly dif ferent between the S288c and
YJM789 branches (Table 4).
The relaxation of selection intensity due to reduction of
ef fective population size is expected to lead to increased evo-
lutionary rate genome-wide. Adaptive evolution and directional
relaxation of selection due to growth environment changes are
ex pected to lead to evolutionary rate increase for specific genes.
The observed increase in evolutionary rate in the laboratory
strain might be caused by a mixture of these factors. The
observed patterns are consistent with laboratory cultivation.
The laboratory growth conditions are extremely different f rom
the ones in the wild. Streaking and picking of single clones is
c ommon during yeast experimentation and leads to a severe
reduction in the effective population size of the laboratory strain.
It is thus likely that laboratory domestication contributes to the
observations made in this study. Nevertheless, the mysterious
origin of the laboratory strain S288c makes it currently difficult
to prove that all of the observed evolutionary rate increase did
oc cur in the laboratory. If laboratory cultivation and possible
industrial domestication did cause the increased evolutionary
rate, the results of this study, especially the greater increase in
nonsynony mous evolutionary rate for genes under stronger
negative selection, imply an evolution of laboratory model
organ isms away from their wild c ounterparts. This finding has
implications for all laboratory model organisms, questioning the
relevanc y of the models especially when extensive laboratory
cultivation has occurred. Because livestock and crop species
domesticated by humans went through severe bottlenecks as
well, the results here also shed light on the evolution of these
organ isms.
We thank Tom Nag ylaki, Zhiheng Yang, Martin K reitman,
Elizabeth Winzeler, Jian Lu, Jerel Davis, and Cristian Castillo-Dav is for
help, discussions, and comments. This work was supported by National
Institutes of Health Grants HG02052, HG00205 (to R.W.D.), and
GM068717 (to R.W.D and L.M.S.).
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Table 4. Direction of synonymous codon change in the S288c and YJM789 branches
Preferred to unpreferred* Unpreferred to preferred
500 genes with the
strongest codon usage bias Rest of the genes
500 genes with the
strongest codon usage bias Rest of the genes
S288c 236 1,908 160 1,767
YJM789 203 1,951 153 1,682
S288cYJM789 1.16 0.98 1.05 1.05
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2
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Gu et al. PNAS
January 25, 2005
vol. 102
no. 4
1097
EVOLUTION
    • "This may also have contributed to the genetic impoverishment of the African rice. A potential consequence of a strong domestication bottleneck is the accumulation of deleterious mutations as already observed in dog (Bj€ ornerfeldt et al. 2006; Cruz et al. 2008), yeast (Gu et al. 2005) and yak (Wang et al. 2011). The effect could be increased by hitch hiking of deleterious alleles especially in low recombining selfing species (Hartfield & Otto 2011; Hartfield & Glémin 2014). "
    [Show abstract] [Hide abstract] ABSTRACT: The African cultivated rice (Oryza glaberrima) was domesticated in West Africa 3,000 years ago. Although less cultivated than the Asian rice (O. sativa), O. glaberrima landraces often display interesting adaptation to rustic environment (e.g., drought). Here, using RNA-seq technology we were able to compare more than 12,000 transcripts between 9 O. glaberrima, 10 wild O. barthii and one O. meridionalis individuals. With a synonymous nucleotide diversity πs = 0.0006 per site, O. glaberrima appears as the least genetically diverse crop grass ever documented. Using Approximate Bayesian Computation, we estimated that O. glaberrima experienced a severe bottleneck during domestication. This demographic scenario almost fully accounts for the pattern of genetic diversity across O. glaberrima genome as we detected very few outliers regions where positive selection may have further impacted genetic diversity. Moreover, the large excess of derived non-synonymous substitution that we detected suggests that the O. glaberrima population suffered from the “cost of domestication”. In addition, we used this genome-scale dataset to demonstrate that (i) O. barthii genetic diversity is positively correlated with recombination rate and negatively with gene density; (ii) expression level is negatively correlated with evolutionary constraint and (iii) one region on chromosome 5 (position 4-6 Mb) exhibits a clear signature of introgression with a yet unidentified Oryza species. This work represents the first genome-wide survey of the African rice genetic diversity and paves the way for further comparison between the African and the Asian rice, notably regarding the genetics underlying domestication traits.This article is protected by copyright. All rights reserved.
    Full-text · Article · Mar 2014
    • "In conclusion, we demonstrate that variation in an important TF is responsible for major phenotypic changes in yeast. Previous studies have highlighted the elevated levels of nonsynonymous changes in TFs among different yeast strains (Gu et al. 2005). Since many human TFs and other regulatory proteins are also polymorphic, it is likely that some of these potential master variators may also be responsible for phenotypic differences, and thus this may be a general mechanism for mediating extensive regulatory (e.g., expression and binding QTLs) and phenotypic variation in all eukaryotes. "
    [Show abstract] [Hide abstract] ABSTRACT: Genetic basis of phenotypic differences in individuals is an important area in biology and personalized medicine. Analysis of divergent Saccharomyces cerevisiae strains grown under different conditions revealed extensive variation in response to both drugs (e.g., 4-nitroquinoline 1-oxide [4NQO]) and different carbon sources. Differences in 4NQO resistance were due to amino acid variation in the transcription factor Yrr1. Yrr1(YJM789) conferred 4NQO resistance but caused slower growth on glycerol, and vice versa with Yrr1(S96), indicating that alleles of Yrr1 confer distinct phenotypes. The binding targets of Yrr1 alleles from diverse yeast strains varied considerably among different strains grown under the same conditions as well as for the same strain under different conditions, indicating that distinct molecular programs are conferred by the different Yrr1 alleles. Our results demonstrate that genetic variations in one important control gene (YRR1), lead to distinct regulatory programs and phenotypes in individuals. We term these polymorphic control genes "master variators."
    Full-text · Article · Feb 2014
    • "These strains are often difficult or impossible to sporulate, which suggests that the ability to undergo sexual cycle degenerates in human-made environments (Johnston 1994). An example of a likely joint action of these factors—smaller population size, benign and specific environment, possible adaptation, and asexual reproduction—has been provided by a study in which a laboratory strain of confirmed history of “domestication” was found to undergo an accelerated rate of molecular evolution, demonstrating considerable relaxation of the purifying selection (Gu et al. 2005). "
    [Show abstract] [Hide abstract] ABSTRACT: Crosses between inbred but unrelated individuals often result in an increased fitness of the progeny. This phenomenon is known as heterosis and was reported both for wild and domesticated populations of plants and animals. Analysis of heterosis is often hindered by the fact that the genetic relatedness between analyzed organisms is known only approximately. We studied a collection of Saccharomyces cerevisiae isolates from wild and human-created habitats whose genomes were sequenced and thus their relatedness is fully known. We reasoned that if these strains accumulated different deleterious mutations at a roughly constant rate, then heterosis should be most visible in F1 heterozygotes from the least related parents. We found that heterosis was substantial and positively correlated with sequence divergence, but only in domesticated strains. More than eighty percent of the heterozygous hybrids were more fit than expected from the mean of their homozygous parents, and about three quarters of those exceeded even the fittest parent. Our results support the notion that domestication brings about relaxation of selection and accumulation of deleterious mutations. However, other factors may have contributed as well. In particular, the observed buildup of genetic load might be facilitated by a decrease and not increase in the rate of inbreeding.
    Full-text · Article · Dec 2013
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