Nature 458, 337-341 (19 March 2009) | doi:10.1038/nature07743; Received 18 June 2008; Accepted 22 December 2008; Published online 11 February 2009

Population genomics of domestic and wild yeasts

Gianni Liti1,9, David M. Carter2,9, Alan M. Moses2,3, Jonas Warringer4, Leopold Parts2, Stephen A. James5, Robert P. Davey5, Ian N. Roberts5, Austin Burt6, Vassiliki Koufopanou6, Isheng J. Tsai6, Casey M. Bergman7, Douda Bensasson7, Michael J. T. O'Kelly8, Alexander van Oudenaarden8, David B. H. Barton1, Elizabeth Bailes1, Alex N. Nguyen3, Matthew Jones2, Michael A. Quail2, Ian Goodhead2,10, Sarah Sims2, Frances Smith2, Anders Blomberg4, Richard Durbin2,9 & Edward J. Louis1,9

  1. Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
  2. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
  3. Department of Cell & Systems Biology, University of Toronto, Ontario M5S 2J4, Canada
  4. Department of Cell and Molecular Biology, Lundberg Laboratory, University of Gothenburg, Medicinaregatan 9c, 41390 Gothenburg, Sweden
  5. National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
  6. Division of Biology, Imperial College London, Silwood Park, Ascot SL5 7PY, UK
  7. Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
  8. Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
  9. These authors contributed equally to this work.
  10. Present address: School of Biological Sciences, University of Liverpool, Liverpool LG9 3BX, UK.

Correspondence to: Richard Durbin2,9Edward J. Louis1,9 Correspondence and requests for materials should be addressed to R.D. (Email: rd@sanger.ac.uk) or E.J.L. (Email: ed.louis@nottingham.ac.uk).

Since the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions3, 4, population structure5, 6, 7, 8 and sexual versus asexual reproduction9, 10. Less well understood at the whole genome level are the evolutionary processes acting within populations and species that lead to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to fourfold or more coverage of the genome sequences of over seventy isolates of the baker's yeast S. cerevisiae and its closest relative, Saccharomyces paradoxus. We examine variation in gene content, single nucleotide polymorphisms, nucleotide insertions and deletions, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. S. paradoxus populations are well delineated along geographic boundaries, whereas the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.


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