Habitat predicts levels of genetic admixture in Saccharomyces cerevisiae

G3: Genes, Genomes, Genetics

Volumn 7, Issue 9, 2017, Pages 2919-2929

  Tilakaratna, Viranga ^a   Bensasson, Douda ^b  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

Admixture; Hybridization; Introgression; Mosaic; Outcrossing; Yeast

Indexed keywords

ARTICLE; BAYES THEOREM; CENTROMERE; CONTROLLED STUDY; DNA SEQUENCE; DOMESTICATION; EUROPE; FOREST; FRUIT; FUNGAL GENETICS; FUNGAL STRAIN; FUNGUS ISOLATION; GENE LOCUS; GENETIC ADMIXTURE; HABITAT; INFECTION; NONHUMAN; NORTH AFRICA; OAK; PHYLOGENY; POPULATION STRUCTURE; SACCHAROMYCES CEREVISIAE; WINE; YEAST; BIOLOGICAL MODEL; CLASSIFICATION; CROSS BREEDING; ECOSYSTEM; GENETIC VARIATION; GENETICS; HYBRIDIZATION; MOLECULAR EVOLUTION; POPULATION GENETICS;

CROSSES, GENETIC; ECOSYSTEM; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENETICS, POPULATION; HYBRIDIZATION, GENETIC; MODELS, GENETIC; PHYLOGENY; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA;

EID: 85029093726     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.117.041806     Document Type: Article

References (60)

1. Almeida, P., C. Gonçalves, S. Teixeira, D. Libkind, M. Bontrager et al., 2014 A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum. Nat. Commun. 5: 4044.
2. Almeida, P., R. Barbosa, P. Zalar, Y. Imanishi, K. Shimizu et al., 2015 A population genomics insight into the Mediterranean origins of wine yeast domestication. Mol. Ecol. 24: 5412-5427.
3. Amberg, D., D. Burke, and J. Strathern, 2005 Methods in Yeast Genetics: A Cold Spring Harbor Laboratory Course Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
4. Avise, J., 1994 Molecular Markers, Natural History and Evolution. Chapman & Hall, New York.
5. Barbosa, R., P. Almeida, S. V. B. Safar, R. O. Santos, P. B. Morais et al., 2016 Evidence of natural hybridization in Brazilian wild lineages of Saccharomyces cerevisiae. Genome Biol. Evol. 8: 317-329.
6. Beekman, M., and F. L. W. Ratnieks, 2000 Long-range foraging by the honey-bee, Apis mellifera L. Funct. Ecol. 14: 490-496.
7. Bensasson, D., 2011 Evidence for a high mutation rate at rapidly evolving yeast centromeres. BMC Evol. Biol. 11: 211.
8. Bensasson, D., M. Zarowiecki, A. Burt, and V. Koufopanou, 2008 Rapid evolution of yeast centromeres in the absence of drive. Genetics 178: 2161-2167.
9. Bonfield, J. K., K. F. Smith, and R. Staden, 1995 A new DNA sequence assembly program. Nucleic Acids Res. 23: 4992-4999.
10. Brandvain, Y., A. M. Kenney, L. Flagel, G. Coop, and A. L. Sweigart, 2014 Speciation and introgression between Mimulus nasutus and Mimulus guttatus. PLoS Genet. 10: e1004410.
11. Buser, C. C., R. D. Newcomb, A. C. Gaskett, andM. R. Goddard, 2014 Niche construction initiates the evolution of mutualistic interactions. Ecol. Lett. 17: 1257-1264.
12. Cherry, J. M., E. L. Hong, C. Amundsen, R. Balakrishnan, G. Binkley et al., 2011 Saccharomyces genome database: the genomics resource of budding yeast. Nucleic Acids Res. 40: D700-D705.
13. Corbett-Detig, R., and R. Nielsen, 2017 A hidden Markov model approach for simultaneously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy. PLoS Genet. 13: e1006529.
14. Coyne, J. A., and B. Milstead, 1987 Long-distance migration of Drosophila. 3. Dispersal of D. melanogaster Alleles from a Maryland Orchard. Am. Nat. 130: 70-82.
15. Cromie, G. A., K. E. Hyma, C. L. Ludlow, C. Garmendia-Torres, T. L. Gilbert et al., 2013 Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq. G3 (Bethesda) 3: 2163-2171.
16. Cubillos, F. A., E. J. Louis, and G. Liti, 2009 Generation of a large set of genetically tractable haploid and diploid Saccharomyces strains. FEMS Yeast Res. 9: 1217-1225.
17. Dashko, S., P. Liu, H. Volk, L. Butinar, J. Piškur et al., 2016 Changes in the relative abundance of two Saccharomyces species from Oak forests to wine fermentations. Front. Microbiol. 7: 215.
18. Diezmann, S., and F. S. Dietrich, 2009 Saccharomyces cerevisiae: population divergence and resistance to oxidative stress in clinical, domesticated and wild isolates. PLoS One 4: e5317.
19. Doniger, S., H. Kim, D. Swain, D. Corcuera, M. Williams et al., 2008 A catalog of neutral and deleterious polymorphism in yeast. PLoS Genet. 4: e1000183.
20. Eberlein, C., J. B. Leducq, and C. R. Landry, 2015 The genomics of wild yeast populations sheds light on the domestication of man's best (micro) friend. Mol. Ecol. 24: 5309-5311.
21. Enache-Angoulvant, A., and C. Hennequin, 2005 Invasive Saccharomyces infection: a comprehensive review. Clin. Infect. Dis. 41: 1559-1568.
22. Evanno, G., S. Regnaut, and J. Goudet, 2005 Detecting the number of clusters of individuals using the software structure: a simulation study. Mol. Ecol. 14: 2611-2620.
23. Falush, D., M. Stephens, and J. K. Pritchard, 2003 Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
24. Fay, J. C., and J. A. Benavides, 2005 Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genet. 1: e5.
25. Felsenstein, J., and G. A. Churchill, 1996 A hidden Markov Model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13: 93-104.
26. Gallone, B., J. Steensels, T. Prahl, L. Soriaga, V. Saels et al., 2016 Domestication and divergence of Saccharomyces cerevisiae Beer yeasts. Cell 166: 1397-1410. e16.
27. Gayevskiy, V., S. Klaere, S. Knight, and M. R. Goddard, 2014 ObStruct: a method to objectively analyse factors driving population structure using Bayesian ancestry profiles. PLoS One 9: e85196.
28. Goddard, M. R., and D. Greig, 2015 Saccharomyces cerevisiae: a nomadic yeast with no niche? FEMS Yeast Res. 15: fov009.
29. Goddard, M. R., N. Anfang, R. Tang, R. C. Gardner, and C. Jun, 2010 A distinct population of Saccharomyces cerevisiae in New Zealand: evidence for local dispersal by insects and human-aided global dispersal in oak barrels. Environ. Microbiol. 12: 63-73.
30. Gonçalves, M., A. Pontes, P. Almeida, R. Barbosa, M. Serra et al., 2016 Distinct domestication trajectories in top-fermenting beer yeasts and wine yeasts. Curr. Biol. 26: 2750-2761.
31. Gouy, M., S. Guindon, and O. Gascuel, 2010 SeaView Version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 27: 221-224.
32. Harris, K., and R. Nielsen, 2016 The genetic cost of Neanderthal introgression. Genetics 203: 881-891.
33. Hubisz, M. J., D. Falush, M. Stephens, and J. K. Pritchard, 2009 Inferring weak population structure with the assistance of sample group information. Mol. Ecol. Resour. 9: 1322-1332.
34. Hufford, M. B., P. Lubinksy, T. Pyhäjärvi, M. T. Devengenzo, N. C. Ellstrand et al., 2013 The genomic signature of crop-wild introgression in Maize. PLoS Genet. 9: e1003477.
35. Hyma, K. E., and J. C. Fay, 2013 Mixing of vineyard and oak-tree ecotypes of Saccharomyces cerevisiae in North American vineyards. Mol. Ecol. 22: 2917-2930.
36. Kellis, M., N. Patterson, M. Endrizzi, B. Birren, and E. S. Lander, 2003 Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
37. Knight, S. J., and M. R. Goddard, 2016 Sporulation in soil as an overwinter survival strategy in Saccharomyces cerevisiae. FEMS Yeast Res. 16: fov102.
38. Koufopanou, V., J. Hughes, G. Bell, and A. Burt, 2006 The spatial scale of genetic differentiation in a model organism: the wild yeast Saccharomyces paradoxus. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361: 1941-1946.
39. Leducq, J. B., L. Nielly-Thibault, G. Charron, C. Eberlein, J. P. Verta et al., 2016 Speciation driven by hybridization and chromosomal plasticity in a wild yeast. Nat. Microbiol. 1: 15003.
40. Liti, G., D.M.Carter, A. M. Moses, J. Warringer, L. Parts et al., 2009 Population genomics of domestic and wild yeasts. Nature 458: 337-341.
41. Ludlow, C. L., G. A. Cromie, C. Garmendia-Torres, A. Sirr, M. Hays et al., 2016 Independent origins of yeast associated with coffee and cacao fermentation. Curr. Biol. 26: 965-971.
42. Marshall, F. B., K. Dobney, T. Denham, and J. M. Capriles, 2014 Evaluating the roles of directed breeding and gene flow in animal domestication. Proc. Natl. Acad. Sci. USA 111: 6153-6158.
43. Nunney, L., 1996 The colonization of oranges by the Cosmopolitan Drosophila. Oecologia 108: 552-561.
44. Paradis, E., 2011 Analysis of Phylogenetics and Evolution with R, Ed. 2. Springer, New York.
45. Pool, J. E., R. B. Corbett-Detig, R. P. Sugino, K. A. Stevens, C. M. Cardeno et al., 2012 Population genomics of Sub-Saharan Drosophila melanogaster: African diversity and Non-African admixture. PLoS Genet. 8: e1003080.
46. Posada, D., and K. A. Crandall, 2002 The effect of recombination on the accuracy of phylogeny estimation. J. Mol. Evol. 54: 396-402.
47. Pritchard, J. K., M. Stephens, and P. Donnelly, 2000 Inference of population structure using Multilocus genotype data. Genetics 155: 945-959.
48. Reuter, M., G. Bell, and D. Greig, 2007 Increased outbreeding in yeast in response to dispersal by an insect vector. Curr. Biol. 17: R81-R83.
49. Robinson, H. A., A. Pinharanda, and D. Bensasson, 2016 Summer temperature can predict the distribution of wild yeast populations. Ecol. Evol. 6: 1236-1250.
50. Rosenzweig, F., and G. Sherlock, 2014 Editorial: experimental evolution: prospects and challenges. Genomics 104: v-vi.
51. Saitou, N., and M. Nei, 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
52. Sampaio, J. P., and P. Gonçalves, 2008 Natural populations of Saccharomyces kudriavzevii in Portugal are associated with Oak Bark and are sympatric with S. cerevisiae and S. paradoxus. Appl. Environ. Microbiol. 74: 2144-2152.
53. Sankararaman, S., S. Mallick, M. Dannemann, K. Prüfer, J. Kelso et al., 2014 The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507: 354-357.
54. Scannell, D. R., O. A. Zill, A. Rokas, C. Payen, M. J. Dunham et al., 2011 The awesome power of yeast evolutionary genetics: new genome sequences and strain resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda) 1: 11-25.
55. Schwartz, M. K., and K. S. McKelvey, 2009 Why sampling scheme matters: the effect of sampling scheme on landscape genetic results. Conserv. Genet. 10: 441.
56. Sniegowski, P. D., P. G. Dombrowski, and E. Fingerman, 2002 Saccharomyces cerevisiae and Saccharomyces paradoxus coexist in a natural woodland site in North America and display different levels of reproductive isolation from European conspecifics. FEMS Yeast Res. 1: 299-306.
57. Stamatakis, A., 2014 RAxML Version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313.
58. Stefanini, I., L. Dapporto, J. L. Legras, A. Calabretta, M. Di Paola et al., 2012 Role of social wasps in Saccharomyces cerevisiae ecology and evolution. Proc. Natl. Acad. Sci. USA 109: 13398-13403.
59. Wang, Q. M., W. Q. Liu, G. Liti, S. A.Wang, and F. Y. Bai, 2012 Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity. Mol. Ecol. 21: 5404-5417.
60. Whitfield, C. W., S. K. Behura, S. H. Berlocher, A. G. Clark, J. S. Johnston et al., 2006 Thrice out of Africa: ancient and recent expansions of the Honey Bee, Apis mellifera. Science 314: 642-645.