Divergent adaptation and reproductive
isolation in experimental populations of fungi
Saccharomyces cerevisiae
Architecture of microevolutionary change
Jim Anderson
University of Toronto
Environment 1
Speciation Theory
Environment 2
fit
fit
hybrid
fit
Dobzhansky-Muller
incompatibility: the negative
interaction (antagonistic
epistasis) between alleles
from different species
Time
Ecological isolation: the byproduct of adaptation to
divergent environments
Experimental evolution of yeast
Single-cell common ancestor
To ALL variants in this talk
0.1 ml to 9.9
ml each day
= 6.6
generations
unique 20
base barcode
unique 20
base barcode
PCR
forward
KanMX4
URA3 ORF
PCR reverse
Fitness: number of doublings (=log2(N1/N0))
over a period of time
Experimental design
Low glucose
YMM (0.13X glucose)
High salt
YPD + 1M NACL
S1
M7
S2
M8
S3
M9
S4
Progenitor
(P)
M10
S5
M11
S6
M12
•500 generations of evolution in sub-optimal
environments
Dettman et al. Nature 2007.
Six sets of experimental populations and hybrids
S
SM
M
Each set:
S P
PM
P
Fitness effects conditional on high salt and low glucose environments.
Note negative epistasis in hybrids between final evolved populations.
ecological
genetic - negative epistatic (DM) interaction
Total of 270 fitness assays in
competitions with the
progenitor
S
S/P
S/M P/M
M
S
S/P
S/M P/M
M
S
S/P
S/M P/M
M
What are the underlying determinants of
adaptation and reproductive isolation?
• 115 isolates sequenced to 100X depth and scored for SNPs
• 100 to 3000 (ave. ca. 700) SNPs called for each isolate
• Filters
Remove SNPs in experiment ancestor (relative to reference
sequence)
Remove alignment and sequencing artifacts
Remove singletons and doubletons
High-salt
populations
High-salt
populations
High-salt
populations
High-salt
populations
High-salt
populations
High-salt
populations
Low glucose: some things to remember
about S. cerevisiae…
• Unicellular fungus specialized for growth in sugar.
• Favors fermentation over respiration, even in the
presence of oxygen - the Crabtree effect
(Crabtree H.G., 1928).
M8
Diauxic
shift
• Transition from fermentation to
respiration is known as the diauxic shift.
P
- Time -
Low-glucose
populations
Bulk sequencing of S2 and M8 over time
F
r
e
q
u
e
n
c
y
100
100
S2
MKT1e
PMA1-1e
LAP2e
PMA1-2e
MET3e
PMA1-3e
PMA1-4e
0
N
o.
MDS3e
TUP1e
0
C
o
p
y
M8
100
40
100
S2
200
400
500
SGT1e
0
0
100
200
300
400
S2 – competition among
genotypes (clonal interference)
ENA genes
M8 – rare, but powerful
program of adaptation
0
100
200
400
500
500
No genetic hitchhiking
Time in generations
Key players and fitness interactions
S2 and M8 populations
Low glucose
High salt
Proton efflux
PMA1e
(+)
Sodium efflux ENA genes
(-)
MDS3e
Global reg.
transcription
(+)
MKT1e
Global reg.
respiration
N.B. All effects tested among strains
differing ONLY for the alleles in question.
Anderson et al. 2010. Current Biology
Slower change in external pH following glucose addition to
suspensions of starved cells for PMA1e than PMA1a
Ancestor,
no glucose
PMA1e MKT1e
PMA1e
MKT1e
Ancestral
PMA1e external pH changes 0.038 ± 0.005 pH units/min.
PMA1a 0.050 ± 0.006 pH units/min. (P = *0.025)
*0.033)
Internal pH is 6.23 ± 0.03
Internal pH is 6.79 ± 0.02 (P =
Parrieras et al. 2011. Eukaryotic Cell
MDS3e MKT1e expression levels are intermediate or greater than
MDS3e and MKT1e alone for four of seven hexose transporter genes.
DM interaction in low glucose: PMA1e and MKT1e
Two crosses:
MATa PMA1e X MATalpha MKT1e
MATa MKT1e X MATalpha PMA1e
Three tetrads from each cross dissected.
Genome-wide expression profiles show MKT1e and
MDS3e interact through changes in gene expression.
No interaction
with respect to
gene expression
Interaction
with
respect to
expression
(163 genes,
4 glucose
transporters)
Enriched for
genes encoding
mitochondrial
proteins - the
MKT1e effect
Model: reduced expression of HXT genes caused by MKT1e
is exacerbated by the low intracellular pH associated with
PMA1e and this delays entry into the cell division cycle.
Science. 1999 Aug 6;285(5429):901-6
Nature. 2002 Jul 25;418(6896):387-91.
The biotin-labelled, deletion-specific primers (B-U1, BU2-comp, B-D1 and B-D2-comp; see Methods for
structure) are used to amplify the unique UPTAG and
DNTAG sequences from genomic preparations generated
in the fitness-profiling studies.
BIO37
2
Sampl
e
proble
m4
Starting population
Oligonucleotide array
9D
2D
1
5
2
6
3
7
4
8
3D
10D
1D
5D
13
10
14
11
15
12
12D
4D
9D
2D
10D
3D
5D
7D
16
13D
16D
1D
6D
8D
7D
4D
9
11D
14D
16D
15D
11D
14D
6D
8D
13D
15D
12D
Population after treatment
Oligonucleotide array
9D
2D
1
2
3
3D
4
5
6
7
12D
10D
1D
14D
7D
8
5D
12
7D
8D
13D
4D
9
10
11
9D
2D
13
14
15
16
1D
5D
15D
16D
16D
2D
10D
3D
7D
6D
12D
14D
8D
15D
6D
12D
13D
Microarrays hybridized with amplified regions containing UPTAGS and DOWNTAGS
High temperature*
High salt*
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
Glucose limitation*
High pH*
1
2
3
4
1
2
3
4
5
6
7
8
5
6
7
8
9
10
11
12
9
10
11
12
13
14
15
16
13
14
15
16
Interpret which genes are important to growth in
which non-optimal environment*.