Origin
Beer
Wine
Spirits
Saké
Wild
Bio-ethanol
Bread
Laboratory
S.paradoxus(^) Be
lgium
/Germa
ny U
S
0.00
0.50
1.00
0.00
0.50
1.00
0.00
0.50
1.00
0.00
0.50
Estimated ancestry (Q)1.00
Britain US GermanyBelgium/ Mixed Wine Beer 2 Asia Mosaic NS
K=2
K=4
K=6
K=8
A
B C
PC1 (11.7%)
PC2 (9.9%)
−0.15 −0.10 −0.05 0.00 0.05 0.10
-0.1
0.0
0.1
0.2
0.3 Britain
US
Belgium/Germany
Beer 2
MixedWine
Asia
Mosaic
NS
0.005
Beer 1
Lineage
Mixed
Wine
Beer 2
West Africa (WA)
Asia
Britain
US
Belgium/Germany
Clinical
B
rit
ai
n
North America (NA)
Malaysia (M)
Beer^2
W
ine
(^)
(^)
(^)
(^)
Mi
xe
d
Be
er^1
(^) WA
(^) A
sia
NA
(^) M
BE089
WI015
SP003
SP007
WI011
BE049
NCYC3447 LA001
BE095
yjm1273
BE059
SP005
yjm1342
BE046
NCYC3319
BE044
WI012
BE057BE060
BE024
BE096
SA001
BR001
BI005
BE065
WL007
WI006
BE022
BE036
BE070
BE005
SP004
BE078
BE042
SA002
BE084
yjm1450
SP009
BE014
BE063
WI003 SA007
BE069
BE092
WL004
BE008
SP001
BI004
BE093 BE019
BE020
BE079BE010
SP008
BE073
WL005
BI003
BR002 BE001
WL002
BE015
BE028
WI009
NCYC3265
BE090
BE058
yjm244
BE013
LA002
BE094
WI018
BE086
yjm1400
WL001
BE062
BE085
yjm682
BE082
WI005
SA005
BE097
BE064
WI016
WI013
BE031
BE061
BE021
WL003
BE102
BE018
yjm1418
SP002 BE054
BE051
BE099
SA004
BE071
BE101
WI017
BE087
SA003
BE035
BE076
BE041
BE075
BE091
NCYC3467
BE034
BE080
BE100
BE053
BE088
BE077
BE056
BE074
BE066
NCYC3574
BE048
BE050
yjm1242
BE003
SP006
BE007
BE068
BE027
NCYC3570
BE029
BE043
BE038
NCYC3449
BE006
yjm1389
BE039
BE026
BE040
BE055
BE045
BE033WI001
SP011
BE009
WI019
BE072
yjm1447
BE052
WI008
BE016
BE002
BE025
BE011
WI007
SP010
BE012
WI014
yjm1244
WI010
BE030
BR003
BE037
BE083
BE017 BE098
WL006
BE004
BR004
NCYC3581
BE067
WI002
BE047
SA006
BE081
BE023
spar
BI002
BE032
yjm320
NCYC3568
NCYC3445
NCYC3448
NCYC3266
WI004
BI001
Mosaic
Figure 1. Phylogeny and Population Structure of IndustrialS. cerevisiaeStrains
(A) Maximum likelihood phylogenetic tree of allS. cerevisiaestrains sequenced in this project supplemented with a representative set of 24 previously sequenced
strains (Liti et al., 2009; Strope et al., 2015) and usingSaccharomyces paradoxusas an outgroup. Black dots on nodes indicate bootstrap support values <70%.
Color codes indicate origin (names) and lineage (circular bands). The basal splits of the five industrial lineages are indicated with colored dots. Mosaic strains
identified in this study are indicated with black dots next to the strain codes. Branch lengths reflect the average number of substitutions per site. Scale bar, 0.005
substitutions per site.
(B) Population structure identified in the 157 surveyed strains. The vertical axis depicts the fractional representation of resolved populations (colors) within each
strain (horizontal axis, strains listed inFigure S1C) for K = 2, 4, 6, and 8 assumed ancestral populations (where K = 8 maximizes the marginal likelihood and best
explains the data structure). Mosaic strains (i.e., strains that possess <80% ancestry from a single population) are visualized as a separate group.
(C) Principal component projection, using the same set of SNPs as inFigure 1B. Colors represent different populations. WA, West Africa; NA, North America; M,
Malaysia; NS, not specified.
See alsoFigure S1and Tables S1, S2, andS8.
Cell 166 , 1397–1410, September 8, 2016 1399