Population Structure and Reticulate Evolution of Wild and Brewing Yeast

Transcription

1 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

2 Yeasts Eukaryotic microorganisms Kurtzman et al., 2011, adapted from Dujon, 2009

3 Yeasts Eukaryotic microorganisms Important for their biotechnological applications wine beer cider Kurtzman et al., 2011, adapted from Dujon, 2009 sake bread biofuels

4 Yeasts Eukaryotic microorganisms Important for their biotechnological applications Important model system Kurtzman et al., 2011, adapted from Dujon, 2009

5 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

6 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

7 The Saccharomyces genus S. cerevisiae S. paradoxus S. mikatae S. kudriavzevii S. arboricola S. uvarum Scannell et al S. eubayanus

8 The Saccharomyces genus S. cerevisiae S. paradoxus S. mikatae S. kudriavzevii ~19% aa S. arboricola S. uvarum Dujon et al S. eubayanus

9 Reticulate evolution: recombination S. cerevisiae S. paradoxus Gene Sp1 S. mikatae Gene SpxSk S. kudriavzevii Gene Sk1 S. arboricola S. uvarum S. eubayanus Peris et al. Mol Ecol (Early view), Peris et al. In preparation

10 Reticulate evolution: introgression S. cerevisiae Chr Sc XIV S. paradoxus S. mikatae Chr Sp XIV S. kudriavzevii S. arboricola S. uvarum Liti et al. 2006, Dunn et al S. eubayanus

11 Reticulate evolution: hybridization S. cerevisiae S. paradoxus S. pastorianus S. mikatae S. kudriavzevii S. bayanus S. arboricola S. uvarum S. eubayanus Gonzalez et al Dunn et al Peris et al. 2012a,b,c Libkind et al. 2010

12 Major questions to be addressed How diverse is Saccharomyces eubayanus and its hybrids?

13 Major questions to be addressed How diverse is Saccharomyces eubayanus and its hybrids? Which ecological factors drive population/species differentiation?

14 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?

15 S. eubayanus samples 3 strains North America Lager Brewing Strains 18/142 strains Patagonia, Argentina S. pastorianus S. pastorianus Saaz group: CBS 1503 Frohberg group: W34/70 S. bayanus CBS 380, CBS 1546, NBRC 1948

16 Concatenated ML/By phylogenetic tree Bs/Bs/PP S. eubayanus 0.8% S. uvarum yhct104 99/100/1 yhct96 70/72/ /100/1 98/92/ ( ) 0.36 ( ) 0.31 ( ) ( ) ( ) 63/63/ /92/1 51/53/ ( ) ( ) yhct101 yhct114 yhct90 yhct99 yhct72 yhks210 yhks212 yhks211 CBS7001 yhct105 yhct91 yhct88 yhct70 yhct107 yhct94 yhct61 yhct92 W34_70 CBS 1503 yhct63 yhct62 yhct76 PATAGONIA Clade A NORTH AMERICA Clade B PATAGONIA - LAGER Clade C 9 nuclear genes ~6.78Kbp 0.005

17 Concordance factors Av CF (95%CI) Bs/Bs/PP S. eubayanus S. uvarum yhct104 99/100/1 yhct96 70/72/ /100/1 98/92/ ( ) 0.36 ( ) 0.31 ( ) ( ) ( ) 63/63/ /92/1 51/53/ ( ) ( ) yhct101 yhct114 yhct90 yhct99 yhct72 yhks210 yhks212 yhks211 CBS7001 yhct105 yhct91 yhct88 yhct70 yhct107 yhct94 yhct61 yhct92 W34_70 CBS 1503 yhct63 yhct62 yhct76 PATAGONIA Clade A NORTH AMERICA Clade B PATAGONIA - LAGER Clade C 0.005

18 Species tree vs gene trees S. eubayanus S. uvarum yhct104 99/100/1 yhct96 70/72/ /100/1 98/92/ ( ) 0.36 ( ) 0.31 ( ) ( ) ( ) 63/63/ /92/1 51/53/ ( ) ( ) yhct101 yhct114 yhct90 yhct99 yhct72 yhks210 yhks212 yhks211 CBS7001 yhct105 yhct91 yhct88 yhct70 yhct107 yhct94 yhct61 yhct92 W34_70 CBS 1503 yhct63 yhct62 yhct76 PATAGONIA NORTH AMERICA PATAGONIA - LAGER A S. eubayanus S. uvarum (0.25,0.75) 100/100/ /53/ (0,0.5) 0.48 (0.25,0.5) 90/90/ (0.5,0.75) 99/98/ (0,0.5) 69/50/0.59 B 0.01 yhct70 yhct107 yhct62 yhct92 yhct61 CBS 1503 W34_70 yhct105 yhct63 yhct76 yhct94 yhct91 yhct88 yhct99 yhct90 yhct114 yhct72 yhks210 yhks211 yhks212 yhct101 yhct104 CBS7001 yhct96 S. eubayanus S. uvarum PATAGONIA - LAGER PATAGONIA (0.5,1) 88/96/ (0.25,5) 87/87/ (0.5,1) 100/100/ (0,0.75) 76/71/ (0.5,0.75) 96/97/0.99 NORTH AMERICA CBS7001 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 PATAGONIA - LAGER PATAGONIA NORTH AMERICA

19 Population structure 0.8% yhct104 99/100/1 yhct96 70/72/ /100/1 98/92/ ( ) 0.36 ( ) 0.31 ( ) ( ) ( ) 63/63/ /92/1 51/53/ ( ) ( ) yhct101 yhct114 yhct90 yhct99 yhct72 yhks210 yhks212 yhks211 CBS7001 yhct105 yhct91 yhct88 yhct70 yhct107 yhct94 yhct61 yhct92 W34_70 CBS 1503 yhct63 yhct62 yhct76 PATAGONIA NORTH AMERICA PATAGONIA - LAGER K=2 Patagonia B (Lager) Patagonia A Fst = 0.73 AMOVA: p-value <

20 Phylogenetic network interpretation Gene A Gene B Gene C Gene D Holland et al. 2008

21 Phylogenetic network interpretation Gene A Gene B Gene C Gene D Holland et al. 2008

22 Phylogenetic network interpretation Gene A Gene B Gene C Gene D Holland et al. 2008

23 Phylogenetic networks S. uvarum W34/70 CBS1503 CBS380 CBS1546 NBRC1948 S. eubayanus

24 History reconstruction No IBD No IBE Diverged Nothofagus trees PA PB(L) kya

25 Travel or Eurasian close relative? 8ºC kya PA Eurasian? PB(L) Lager

26 Hybridization & lager brewing Brewing started around 10kya Cross with ale S. cer PA PB(L) Eurasian? Lager

27 Admixture 8ºC PA PB(L) NA

28 Exploration of new trees F. grandifolia A. saccharum 8ºC PA PB(L) NA

29 The Saccharomyces populations Liti et al Nature Wang et al Mol Ecol <1% Liti et al Nature %? -> ~1% <1% 1.8% S. mikatae S. cerevisiae Koufopanou et al RPBS Europe A Far East America B America C S. paradoxus Leducq et al RPBS 3.5% 1% Europe Asia A Asia B S. kudriavzevii? Hittinger et al S. arboricola 7%? S. uvarum Peris et al Mol Ecol (Early view) 0.8% Patagonia A Patagonia B (Lager) S. eubayanus

30 Conclusions Concatenated data is misleading.

31 Conclusions Concatenated data is misleading. S. eubayanus are native, but not endemic to South America.

32 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.

33 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.

34 Lab members Acknowledgements Collaborators Dr. Chris T. Hittinger Dr. Diego Libkind Dr. William G. Alexander Dr. José Paulo Sampaio Kayla Sylvester Yeast Exploration and Analysis Science Team Dr. Paula Gonçalves Amanda Hulfachor

35 Thank you