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transcript
Population Structure and Reticulate Evolution of
Wild and Brewing Yeast
David Peris
University of Wisconsin, Madison Peris D, Sylvester K, Libkind D, Sampaio JP, Gonçalves P, Alexander WG, Hittinger CT
Midwest Ecology & Evolution Conference
3-1-2014
Yeasts Eukaryotic microorganisms
Important for their biotechnological
applications
Kurtzman et al., 2011, adapted from Dujon, 2009
wine beer
sake bread
cider
biofuels
Yeasts Eukaryotic microorganisms
Important for their biotechnological
applications
Important model system
Kurtzman et al., 2011, adapted from Dujon, 2009
Yeasts Eukaryotic microorganisms
Important for their biotechnological
applications
Important model system
Ecology of yeasts has been largely
ignored
Kurtzman et al., 2011, adapted from Dujon, 2009
Yeasts Eukaryotic microorganisms
Important for their biotechnological
applications
Important model system
Ecology of yeasts has been largely
ignored
Kurtzman et al., 2011, adapted from Dujon, 2009
The Saccharomyces genus
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
S. eubayanus Scannell et al. 2011
The Saccharomyces genus
Dujon et al. 2006
~19% aa
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
S. eubayanus
Peris et al. Mol Ecol (Early view), Peris et al. In preparation
Reticulate evolution: recombination
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
S. eubayanus
Gene Sp1
Gene Sk1
Gene SpxSk
Liti et al. 2006, Dunn et al. 2012
Reticulate evolution: introgression
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
S. eubayanus
Chr Sc XIV
Chr Sp XIV
Gonzalez et al. 2008
Dunn et al. 2008
Peris et al. 2012a,b,c
Libkind et al. 2010
Reticulate evolution: hybridization
S. pastorianus S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
S. eubayanus
S. bayanus
How diverse is Saccharomyces eubayanus and its hybrids?
Which ecological factors drive population/species
differentiation?
Major questions to be addressed
How diverse is Saccharomyces eubayanus and its hybrids?
Which ecological factors drive population/species
differentiation?
What is the role of reticulate evolution in the adaptation to
new natural/artificial environments?
Major questions to be addressed
S. eubayanus samples
18/142 strains Patagonia, Argentina
3 strains North America
S. pastorianus
S. bayanus
S. pastorianus
CBS 380, CBS 1546, NBRC 1948
Saaz group: CBS 1503 Frohberg group: W34/70
Lager Brewing Strains
Concatenated ML/By phylogenetic tree
Bs/Bs/PP
0.8%
70/72/0.99
99/100/1
99/100/1
98/92/1
63/63/0.99
94/92/1
51/53/0.88
yHCT104
yHCT96
yHCT101
yHCT114
yHCT90
yHCT99
yHCT72
0.005
yHKS210
yHKS212
yHKS211
yHCT105
yHCT91
yHCT88
yHCT70
yHCT107
yHCT94
yHCT61
yHCT92
W34_70
CBS 1503
yHCT63
yHCT62
yHCT76
CBS7001
PA
TA
GO
NIA
PA
TA
GO
NIA
-LA
GE
RN
OR
TH
AM
ER
ICA
0.410
(0.25-0.625)
0.36
(0.25-0.5)
0.31
(0.25-0.5)
0.379
(0.25-0.625)
0.364
(0.25-0.5)
0.149
(0-0.375)
0.63
(0.5-0.75)
W34_70
CBS 1503
Clade A
Clade B
Clade C
S. uvarum
S. eubayanus
9 nuclear genes ~6.78Kbp
Concordance factors
S. uvarum
S. eubayanus
70/72/0.99
99/100/1
99/100/1
98/92/1
63/63/0.99
94/92/1
51/53/0.88
yHCT104
yHCT96
yHCT101
yHCT114
yHCT90
yHCT99
yHCT72
0.005
yHKS210
yHKS212
yHKS211
yHCT105
yHCT91
yHCT88
yHCT70
yHCT107
yHCT94
yHCT61
yHCT92
W34_70
CBS 1503
yHCT63
yHCT62
yHCT76
CBS7001
PA
TA
GO
NIA
PA
TA
GO
NIA
-LA
GE
RN
OR
TH
AM
ER
ICA
0.410
(0.25-0.625)
0.36
(0.25-0.5)
0.31
(0.25-0.5)
0.379
(0.25-0.625)
0.364
(0.25-0.5)
0.149
(0-0.375)
0.63
(0.5-0.75)
Bs/Bs/PP
Av CF (95%CI)
Clade A
Clade B
Clade C
W34_70
CBS 1503
Species tree vs gene trees
S. uvarum
S. eubayanus
70/72/0.99
99/100/1
99/100/1
98/92/1
63/63/0.99
94/92/1
51/53/0.88
yHCT104
yHCT96
yHCT101
yHCT114
yHCT90
yHCT99
yHCT72
0.005
yHKS210
yHKS212
yHKS211
yHCT105
yHCT91
yHCT88
yHCT70
yHCT107
yHCT94
yHCT61
yHCT92
W34_70
CBS 1503
yHCT63
yHCT62
yHCT76
CBS7001
PA
TA
GO
NIA
PA
TA
GO
NIA
-LA
GE
RN
OR
TH
AM
ER
ICA
0.410
(0.25-0.625)
0.36
(0.25-0.5)
0.31
(0.25-0.5)
0.379
(0.25-0.625)
0.364
(0.25-0.5)
0.149
(0-0.375)
0.63
(0.5-0.75)
PA
TA
GO
NIA
NORTH
AMERICAPA
TA
GO
NIA
-LA
GE
R
88/96/0.99
0.728
(0.5,1)
87/87/0.99
100/100/0.99
76/71/0.94
96/97/0.99
0.291
(0.25,5)
0.734
(0.5,1)
0.348
(0,0.75)
0.575
(0.5,0.75)
yHCT62
yHCT76
yHKS210
yHKS211
yHKS212
yHCT94
yHCT63
yHCT61
yHCT92
yHCT105
yHCT70
yHCT107
yHCT88
yHCT91
CBS 1503
W34_70
yHCT104
yHCT101
yHCT96
yHCT72
yHCT90
yHCT99
yHCT114
CBS7001
0.01
PA
TA
GO
NIA
NORTH
AMERICA
PA
TA
GO
NIA
-LA
GE
R
46/53/0.99
100/100/0.99
90/90/0.99
99/98/0.99
69/50/0.59
0.514
(0.25,0.75)
0.27
(0,0.5)
0.48
(0.25,0.5)
0.715
(0.5,0.75)
0.104
(0,0.5)
yHCT70
yHCT107
yHCT62
yHCT92
yHCT61
CBS 1503
W34_70
yHCT105
yHCT63
yHCT76
yHCT94
yHCT91
yHCT88
yHCT99
yHCT90
yHCT114
yHCT72
yHKS210
yHKS211
yHKS212
yHCT101
yHCT104
yHCT96
CBS7001
0.01
A
B
S. uvarum
S. eubayanus
S. uvarum
S. eubayanus
CBS 1503
W34_70
CBS 1503
W34_70
W34_70
CBS 1503
Population structure
Fst = 0.73 AMOVA: p-value < 10-4
0.8%
70/72/0.99
99/100/1
99/100/1
98/92/1
63/63/0.99
94/92/1
51/53/0.88
yHCT104
yHCT96
yHCT101
yHCT114
yHCT90
yHCT99
yHCT72
0.005
yHKS210
yHKS212
yHKS211
yHCT105
yHCT91
yHCT88
yHCT70
yHCT107
yHCT94
yHCT61
yHCT92
W34_70
CBS 1503
yHCT63
yHCT62
yHCT76
CBS7001
PA
TA
GO
NIA
PA
TA
GO
NIA
-LA
GE
RN
OR
TH
AM
ER
ICA
0.410
(0.25-0.625)
0.36
(0.25-0.5)
0.31
(0.25-0.5)
0.379
(0.25-0.625)
0.364
(0.25-0.5)
0.149
(0-0.375)
0.63
(0.5-0.75)
Patagonia B (Lager) Patagonia A
K=2
W34_70
CBS 1503
Lager
Eurasian?
Brewing started around 10kya
Hybridization & lager brewing
PA
PB(L)
Cross with “ale” S. cer
The Saccharomyces populations
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
S. eubayanus
Europe A
America B
America C
Far East
<1%
2.5-3.5% 1.8%
Leducq et al. 2014 RPBS
Liti et al. 2009 Nature Wang et al. 2012 Mol Ecol <1%
? -> ~1%
?
3.5% 1% Europe
Asia A
Asia B
Peris et al. 2014 Mol Ecol (Early view)
Patagonia A
Patagonia B (Lager) 0.8%
Hittinger et al. 2010
Liti et al. 2009 Nature Koufopanou et al. 2006 RPBS
?
7%
Conclusions
Concatenated data is misleading.
S. eubayanus are native, but not endemic to South America.
Conclusions
Concatenated data is misleading.
S. eubayanus are native, but not endemic to South America.
S. eubayanus is not diverse outside of South America, but it
is involved reticulate events.
Conclusions
Concatenated data is misleading.
S. eubayanus are native, but not endemic to South America.
S. eubayanus is not diverse outside of South America, but it
is involved reticulate events.
Reticulation events in yeast are important.
Lab members Collaborators
Acknowledgements
Yeast Exploration and Analysis
Science Team
Kayla Sylvester
Dr. Chris T. Hittinger Dr. Diego Libkind
Dr. José Paulo Sampaio
Dr. Paula Gonçalves
Dr. William G. Alexander
Amanda Hulfachor