Population Structure and Reticulate Evolution of Wild and Brewing Yeast

David PerisUniversity of Wisconsin, Madison

Peris D, Sylvester K, Libkind D, Sampaio JP, Gonçalves P, Alexander WG, Hittinger CTMidwest Ecology & Evolution Conference

3-1-2014

YeastsEukaryotic microorganisms

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

YeastsEukaryotic microorganisms

Important for their biotechnological applications

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

wine beer

sake bread

cider

biofuels

YeastsEukaryotic microorganisms

Important for their biotechnological applications

Important model system

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

YeastsEukaryotic microorganisms

Important for their biotechnological applications

Important model system

Ecology of yeasts has been largely ignored

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

YeastsEukaryotic 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. eubayanusScannell 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. 2008Dunn et al. 2008

Peris et al. 2012a,b,cLibkind et al. 2010

Reticulate evolution: hybridization

S. pastorianusS. 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 strainsNorth 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

yHKS210yHKS212yHKS211

yHCT105

yHCT91

yHCT88

yHCT70

yHCT107

yHCT94

yHCT61

yHCT92

W34_70

CBS 1503

yHCT63

yHCT62

yHCT76

CBS7001

PA

TAG

ON

IA

PA

TAG

ON

IA -

LAG

ER

NO

RT

HA

ME

RIC

A

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

yHKS210yHKS212yHKS211

yHCT105

yHCT91

yHCT88

yHCT70

yHCT107

yHCT94

yHCT61

yHCT92

W34_70

CBS 1503

yHCT63

yHCT62

yHCT76

CBS7001

PA

TAG

ON

IA

PA

TAG

ON

IA -

LAG

ER

NO

RT

HA

ME

RIC

A

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/PPAv 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

yHKS210yHKS212yHKS211

yHCT105

yHCT91

yHCT88

yHCT70

yHCT107

yHCT94

yHCT61

yHCT92

W34_70

CBS 1503

yHCT63

yHCT62

yHCT76

CBS7001

PA

TAG

ON

IA

PA

TAG

ON

IA -

LAG

ER

NO

RT

HA

ME

RIC

A

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

TAG

ON

IA

NORTHAMERICAP

ATA

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

TAG

ON

IA

NORTHAMERICA

PA

TAG

ON

IA -

LAG

ER

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 = 0.73AMOVA: 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

yHKS210yHKS212yHKS211

yHCT105

yHCT91

yHCT88

yHCT70

yHCT107

yHCT94

yHCT61

yHCT92

W34_70

CBS 1503

yHCT63

yHCT62

yHCT76

CBS7001

PA

TAG

ON

IA

PA

TAG

ON

IA -

LAG

ER

NO

RT

HA

ME

RIC

A

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

CBS1546NBRC1948

W34/70

CBS1503

S. eubayanus

S. uvarum

PA

PB(L) 250-100kya

Diverged

History reconstruction

Nothofagus trees

No IBDNo IBE

Lager

Eurasian?200-40kya8ºC

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 treesA. saccharumF. 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 NatureWang et al. 2012 Mol Ecol <1%

? -> ~1%

?

3.5% 1% Europe

Asia A

Asia B

Peris et al. 2014 Mol Ecol (Early view)

Patagonia APatagonia B (Lager)0.8%

Hittinger et al. 2010

Liti et al. 2009 Nature Koufopanou et al. 2006 RPBS

?

7%

ConclusionsConcatenated data is misleading.

ConclusionsConcatenated data is misleading.

S. eubayanus are native, but not endemic to South America.

ConclusionsConcatenated 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.

ConclusionsConcatenated 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