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

Kurtzman et al., 2011, adapted from Dujon, 2009

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?

Major questions to be addressed

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

Phylogenetic network interpretation

Gene A Gene B Gene C Gene D

Holland et al. 2008

Phylogenetic network interpretation

Gene A Gene B Gene C Gene D

Holland et al. 2008

Phylogenetic network interpretation

Gene A Gene B Gene C Gene D

Holland et al. 2008

Phylogenetic networks

CBS380

CBS1546 NBRC1948

W34/70

CBS1503

S. eubayanus

S. uvarum

PA

PB(L) 250-100kya

Diverged

History reconstruction

Nothofagus trees

No IBD No IBE

Lager

Eurasian? 200-40kya

8ºC

Travel or Eurasian close relative?

PA

PB(L)

Lager

Eurasian?

Brewing started around 10kya

Hybridization & lager brewing

PA

PB(L)

Cross with “ale” S. cer

PA

PB(L) NA

8ºC

Admixture

8ºC

Exploration of new trees A. saccharum F. grandifolia

PA

PB(L) NA

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.

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

Thank you