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ANY fields in biology have progressed by the concentrated study of a select group of model systems. In population and evolutionary genetics, only a
few species such as Drosophila and humans have been
widely adopted, and it might make sense to consider
what other taxa might best complement these. The yeast
Saccharomyces cerevisiae has a number of characteristics
that would seem to make it ideal (Zeyl 2000): (i) It is
already a well-studied model system in biochemistry, cell
biology, classical genetics, and molecular biology; (ii)
genomes can be precisely altered by homologous recombination; and (iii) long-term experiments with large
population sizes and sensitive fitness assays are readily
possible in the laboratory. These features suggest that
one may be more likely to be able to investigate and
interpret the functional significance of natural DNA
sequence variation in this species than in any other
eukaryote. Moreover, it has a relatively small and generich genome, reducing the size of the problem to be
solved. However, there is a problem: S. cerevisiae has
long been associated with humans, and in collecting
strains it is difficult to determine to what extent they
Sequence data from this article have been deposited with the
EMBL/GenBank Data Libraries under accession nos. AJ515177
AJ515216, AJ515322AJ515352, and AJ515430AJ515449.
1
Corresponding author: Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, United Kingdom. E-mail: l.j.johnson@nottingham.ac.uk
2
Present address: Department of Infectious Disease Epidemiology,
Imperial College, London W2 1PG, United Kingdom.
Genetics 166: 4352 ( January 2004)
44
L. J. Johnson et al.
45
TABLE 1
Primer sequences
Gene
STE3 (YKL178c): -pheromone receptor, chromosome 11 STE3-F3: TGG ACA CAT TCA TTA CCT ACC ACG
STE3-ENDR: TTT CTG AAC TAA GCT CAT TTG AAC
STE3-530R*: GAA AAC GAA CAG CAC CAA GG
STE3-989F*: AGG ATT TAC AGC AGG TGG ATG G
STE3-997R*: TTT CAG AAT CGG TAG AGA ATG G
AGA2 (YGL032c): -agglutinin subunit, chromosome 7
STE3
STE2
SAG1
AGA2
A
?
T
T
T
T
T
T
T
T
T
?
?
T
C
.
.
.
.
.
.
.
.
.
?
?
.
G
.
.
.
.
.
.
a
.
.
a
.
.
.
3
4
4
4
4
4
4
4
4
4
4
.
4
4
C
T
T
T
T
T
.
.
.
.
T
T
T
T
A
.
.
.
.
A
G
.
.
.
.
.
.
.
.
.
.
.
G
T
.
.
.
.
C
.
.
.
.
.
.
.
.
G
.
.
.
.
.
T
.
.
.
.
.
.
.
G
A
.
.
.
A
.
.
.
.
.
.
.
.
C
T
T
T
T
T
T
T
T
T
T
T
T
.
T
.
.
.
.
A
.
.
.
.
.
.
.
C
A
.
.
.
.
C
.
.
.
.
.
.
.
.
G
.
.
.
.
C
.
.
.
.
.
.
.
T
A
.
.
.
.
T
.
.
.
.
.
.
.
.
T
.
.
.
.
A
.
.
.
.
.
.
.
A
A
G
G
G
G
G
G
G
G
G
G
G
G
G
C
.
.
.
.
.
T
T
T
.
T
T
T
T
C
T
.
.
.
.
.
.
.
.
.
.
.
.
A
T
.
.
.
.
.
.
.
T
.
.
.
.
C
T
.
.
.
.
.
.
.
T
.
.
.
.
A
.
G
?
G
.
.
.
G
.
.
.
.
.
A
.
G
?
G
.
.
.
G
.
.
.
.
.
G
.
A
A
A
.
.
.
A
.
.
.
.
.
G
T
.
.
.
.
T
T
.
.
.
.
.
.
T
.
.
.
.
T
T
.
.
.
.
.
.
130 108 354 R 17 245 10 792 805 1365 1544 1593 1679 1707 1718 1775 224 837 1106 1382 1387 90 915 1578 346 347
MFA1
Nucleotide polymorphisms found in the initial survey of nine wild isolates and the Type and Danish strains are shown. Also shown, for comparison, are the nucleotides
found in the Far Eastern strains and in S. cerevisiae (S. c). Dots indicate identity to Type. Bases are numbered from the start of the coding sequence; negative numbers
indicate upstream positions. Column R shows number of repeats of the MF1 pheromone unit. Noncoding regions are shown in italic type.
Type
Danish
T8.1
T21.4
T32.1
T62.1
T76.6
Q4.1
Q32.3
Q59.1
Q70.8
FE1
FE2
S. c
Base
MF1
Gene
Polymorphisms
TABLE 2
46
L. J. Johnson et al.
47
TABLE 3
Estimates of nucleotide diversity in S. paradoxus wild isolates
Coding sequence
Noncoding sequence
Gene
Strains
bp
a 103
s 103
bp
103
MFA1
MF1
STE2
STE3
AGA2
SAG1
Total
9
9
9
9
9
8
111
534
1296
1413
264
1956
5534
0
0
0
0.21
0
0
0.07
23.31
6.94
2.16
1.42
0
3.96
3.53
463
150
214
450
221
158
1656
1.2
2.6
1.8
2.5
1.8
3.4
1.7
Average pairwise diversity per nucleotide site at synonymous (s) and nonsynonymous (a) sites of coding
regions and of adjacent noncoding sequence is shown. Noncoding regions considered are upstream of MF1
and SAG1; downstream of MFA1, STE2, and STE3; and 91 bp upstream 130 bp downstream of AGA2. The
STE2 sequence does not include the first 200 bp.
48
L. J. Johnson et al.
49
TABLE 4
Genotypes of 28 wild S. paradoxus isolates
Month
collected
MF1
333, 354, R
MFA1 17
W7
S36.7
T4ba
T8.1a
T18.2
T21.4a
T22.1a
T26.3
T27.3a
T32.1a
T62.1
T68.2a
T76.6a
10/96
12/97
5/98
5/98
5/98
5/98
5/98
7/98
7/98
7/98
7/98
7/98
7/98
TA4
TG4
TG4
TG4
TG4
TG4
TG4
?
TG4
TG4
TA4
TA4
TG4
C
C
T
T
C
T
T
C
T
T
T
T
C
Silkwood Park
TG
?
CG
TT
TG
AC
TG
AC
TG
?
TG
AC
TG
AC
TG
AC
TG
AC
TG
AC
CG
AC
TG
AC
TT
AC
Q4.1
Q6.1
Q14.4a
Q15.1a
Q16.1a
Q31.4a
Q32.3
Q43.5a
Q59.1
Q62.5
Q69.8a
Q70.8a
Q74.4a
Q89.8
Q95.3
9/98
9/98
9/98
9/98
9/98
9/98
9/98
9/98
10/98
10/98
10/98
10/98
10/98
10/98
10/98
TA4
TA4
TA2
AA3
AA3
TG4
TG4
TA4
TG4
TG4
TA2
TA4
TA4
TG4
TG4
C
T
C
C
C
C
C
C
C
C
C
T
C
C
C
ID
STE3
792, 805
STE2
1382, 1387
SAG1
1578
AGA2
346, 347
TFA1
G
G
A
A
A/G
A
A
A
A
A
G
G
G
GGGGGGGTT
GGGGTT
2
3
1
1
3
1
1
1
1
1
2
2
2
G
A
G
A
A
G
A
G
G
G
G
G
G
A
G
TT
TT
GTT
TT
TT
GGGTT
GGGGG-
1
1
2
2
2
2
1
1
1
2
2
2
1
1
1
Bases or repeat numbers are shown for polymorphic sites at seven loci. Numbers under the gene names
indicate polymorphic positions scored (see Table 2). Two MF1 alleles were absent from the nine-isolate set:
both differ from Type sequence by the G A change at base 354; allele 3 has a further T A change at
base 333 and three pheromone repeats. Allele 4 has two pheromone repeats.
a
Isolate IDs with indistinguishable genotypes.
an overrepresentation of genotypes. Evidence for inbreeding comes from the high homozygosity. An assumption in making this inference is that S. paradoxus
in the field behaves as it does in the lab, and in particular
that the diplophase predominates, and so the cells we
isolated are diploid. In principle, an alternative explanation for the lack of heterozygosity is that cells are haploids in nature, but autodiploidize in the early stages of
the isolation procedure. However, we do not consider
it likely that S. paradoxus should change its life cycle so
drastically in response to laboratory conditions. Finally,
evidence for outcrossing comes from the single heterozygote we found plus the genealogical incompatibility
between loci and absence of linkage disequilibrium.
This contrast between the great excess of homozygosity and the absence of linkage disequilibrium between
genes reflects the fact that even small amounts of outcrossing and recombination will randomize alleles at
50
L. J. Johnson et al.
Figure 2.Locations of oak trees from which wild isolates were collected. Superimposed circles indicate isolates from the
same tree. Suspected clones are shown as open circles.
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51
52
L. J. Johnson et al.
APPENDIX
sxt 1 HWi 3 .
2
x0
In our data set there are 7 loci, and the probability that
an individual will be homozygous at all of them is then
p(all homozygous)
x0
i1
sxt 1 HWi3 .
2
x0
i1
When we count only one isolate of each distinct genotype, the data consist of 14 completely homozygous genotypes, two homozygous isolates with unknown STE2
genotype, one homozygous isolate with unknown MF1
genotype, and the heterozygote T18.2. The probability
of observing the entire data set is therefore
p(data) p(all homozygous)14 p(missing STE2)2
p(missing MF1) p(T18.2).
The maximum possible value of this occurs at an outcrossing rate of t 1.1%, with 2-unit support limits of
0.06 and 5%.
We also modeled a mixed-mating population in which
individuals were derived either from mating between
clonemates (autodiploidization) with probability s or
from random outcrossing with probability t. In this case
individuals are either completely homozygous at all loci
or heterozygous at Hardy-Weinberg proportions, and
the probability an individual is homozygous at the ith
locus is
p(homozygous) s t(1 HWi).
With this model the maximum-likelihood outcrossing
rate is 6%, with 2-unit support limits of 0.3 and 23%,
higher than that in the previous model, as a greater
frequency of outcrossing is needed to counterbalance
the more intense inbreeding caused by autodiploidization.