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S.eubayanus & reticulate evolution
The document discusses the population structure and reticulate evolution of wild and brewing yeast, particularly focusing on the Saccharomyces genus and its diversity across different ecological environments. It raises key questions about hybridization, ecological factors driving differentiation, and the role of reticulate evolution in adaptation. The findings highlight the importance of reticulation events in yeast and the limited diversity of Saccharomyces eubayanus outside South America.
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S.eubayanus & reticulate evolution
- 1. Population Structure andReticulate 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
- 2. Yeasts Eukaryotic microorganisms Kurtzman etal., 2011, adapted from Dujon, 2009
- 3. Yeasts Eukaryotic microorganisms Important fortheir biotechnological applications Kurtzman et al., 2011, adapted from Dujon, 2009 wine beer sake bread cider biofuels
- 4. Yeasts Eukaryotic microorganisms Important fortheir biotechnological applications Important model system Kurtzman et al., 2011, adapted from Dujon, 2009
- 5. Yeasts Eukaryotic microorganisms Important fortheir 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 fortheir 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.paradoxus S. mikatae S. arboricola S. kudriavzevii S. uvarum S. cerevisiae S. eubayanus Scannell et al. 2011
- 8. The Saccharomyces genus Dujonet al. 2006 ~19% aa S. paradoxus S. mikatae S. arboricola S. kudriavzevii S. uvarum S. cerevisiae S. eubayanus
- 9. 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
- 10. 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
- 11. 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
- 12. How diverse isSaccharomyces eubayanus and its hybrids? Major questions to be addressed
- 13. How diverse isSaccharomyces eubayanus and its hybrids? Which ecological factors drive population/species differentiation? Major questions to be addressed
- 14. How diverse isSaccharomyces 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
- 15. S. eubayanus samples 18/142strains 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
- 16. Concatenated ML/By phylogenetictree 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 PATAGONIA PATAGONIA-LAGERNORTH AMERICA 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
- 17. 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 PATAGONIA PATAGONIA-LAGERNORTH AMERICA 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
- 18. Species tree vsgene 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 PATAGONIA PATAGONIA-LAGERNORTH AMERICA 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 NORTH AMERICA PATAGONIA-LAGER 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 PATAGONIA NORTH AMERICA PATAGONIA-LAGER 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
- 19. 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 PATAGONIA PATAGONIA-LAGERNORTH AMERICA 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
- 20. Phylogenetic network interpretation GeneA Gene B Gene C Gene D Holland et al. 2008
- 21. Phylogenetic network interpretation GeneA Gene B Gene C Gene D Holland et al. 2008
- 22. Phylogenetic network interpretation GeneA Gene B Gene C Gene D Holland et al. 2008
- 23.
- 24. PA PB(L) 250-100kya Diverged History reconstruction Nothofagustrees No IBD No IBE
- 25. Lager Eurasian? 200-40kya 8ºC Travel or Eurasianclose relative? PA PB(L)
- 26. Lager Eurasian? Brewing started around 10kya Hybridization& lager brewing PA PB(L) Cross with “ale” S. cer
- 27.
- 28. 8ºC Exploration of newtrees A. saccharumF. grandifolia PA PB(L) NA
- 29. 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%
- 30. Conclusions Concatenated data ismisleading.
- 31. Conclusions Concatenated data ismisleading. S. eubayanus are native, but not endemic to South America.
- 32. Conclusions Concatenated data ismisleading. 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 ismisleading. 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 Collaborators Acknowledgements YeastExploration 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
- 35.