A population genomics insight into the Mediterranean origins of wine yeast domestication

Pedro Almeida, Raquel Barbosa, Polona Zalar, Yumi Imanishi, Kiminori Shimizu, Benedetta Turchetti, Jean Luc Legras, Marta Serra, Sylvie Dequin, Arnaud Couloux, Julie Guy, Douda Bensasson, Paula Gonçalves, José Paulo Sampaio

Research output: Contribution to journalArticlepeer-review

95 Citations (Scopus)


The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole-genome data of oak-associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and new geographically delimited populations, including a novel Mediterranean oak population. This population is the closest relative of the wine lineage as shown by a weak population structure and further supported by genomewide population analyses. A coalescent model considering partial isolation with asymmetrical migration, mostly from the wild group into the Wine group, and population growth, was found to be best supported by the data. Importantly, divergence time estimates between the two populations agree with historical evidence for winemaking. We show that three horizontally transmitted regions, previously described to contain genes relevant to wine fermentation, are present in the Wine group but not in the Mediterranean oak group. This represents a major discontinuity between the two populations and is likely to denote a domestication fingerprint in wine yeasts. Taken together, these results indicate that Mediterranean oaks harbour the wild genetic stock of domesticated wine yeasts.

Original languageEnglish
Pages (from-to)5412-5427
Number of pages16
JournalMolecular Ecology
Issue number21
Publication statusPublished - Nov 2015


  • comparative genomics
  • domestication fingerprints
  • microbe domestication
  • microbe population genomics
  • yeast molecular ecology

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