title: Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at noncoding sites.
abstract: In Saccharomyces cerevisiae, the main yeast in wine fermentation, the opportunity to examine divergence at the molecular level between a domesticated lineage and its wild counterpart arose recently due to the identification of the closest relatives of wine strains, a wild population associated with Mediterranean oaks. As genomic data are available for a considerable number of representatives belonging to both groups, we used population genomics to estimate the degree and distribution of nucleotide variation between wine yeasts and their closest wild relatives. We found widespread genomewide divergence, particularly at noncoding sites, which, together with above average divergence in trans-acting DNA binding proteins, may suggest an important role for divergence at the level of transcriptional regulation. Nine outlier regions putatively under strong divergent selection were highlighted by a genomewide scan under stringent conditions. Several cases of introgressions, originating in the sibling species Saccharomyces paradoxus, were also identified in the Mediterranean oak population. FZF1 and SSU1, mostly known for conferring sulphite resistance in wine yeasts, were among the introgressed genes, although not fixed. Because the introgressions detected in our study are not found in wine strains, we hypothesize that ongoing divergent ecological selection segregates the two forms between the different niches. Together, our results provide a first insight into the extent and kind of divergence between wine yeasts and their closest wild relatives.
authors.affiliation: Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
authors.forename: Pedro
authors.initials: P
authors.lastname: Almeida
authors.affiliation: Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
authors.forename: Raquel
authors.initials: R
authors.lastname: Barbosa
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.|Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
authors.forename: Douda
authors.identifier: http://orcid.org/0000-0002-9015-2707
authors.initials: D
authors.lastname: Bensasson
authors.affiliation: Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
authors.forename: Paula
authors.initials: P
authors.lastname: Gonçalves
authors.affiliation: Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
authors.forename: José Paulo
authors.identifier: http://orcid.org/0000-0001-8145-5274
authors.initials: JP
authors.lastname: Sampaio
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D005075:Biological Evolution; D005285:Fermentation; D005828:Genetics, Population; D016681:Genome, Fungal; D005838:Genotype; D020641:Polymorphism, Single Nucleotide; D029963:Quercus / Q000382:microbiology; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D012641:Selection, Genetic; D014920:Wine / Q000382:microbiology*
keywords: 
  Saccharomyces cerevisiae
  ; comparative population genomics; divergent selection; introgression; microbe adaptive evolution; wine yeast domestication