title: Population genomics of domestic and wild yeasts.
abstract: 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 distributions, population structure and sexual versus asexual reproduction. 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.
authors.affiliation: Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
authors.forename: Gianni
authors.initials: G
authors.lastname: Liti
authors.forename: David M
authors.initials: DM
authors.lastname: Carter
authors.forename: Alan M
authors.initials: AM
authors.lastname: Moses
authors.forename: Jonas
authors.initials: J
authors.lastname: Warringer
authors.forename: Leopold
authors.initials: L
authors.lastname: Parts
authors.forename: Stephen A
authors.initials: SA
authors.lastname: James
authors.forename: Robert P
authors.initials: RP
authors.lastname: Davey
authors.forename: Ian N
authors.initials: IN
authors.lastname: Roberts
authors.forename: Austin
authors.initials: A
authors.lastname: Burt
authors.forename: Vassiliki
authors.initials: V
authors.lastname: Koufopanou
authors.forename: Isheng J
authors.initials: IJ
authors.lastname: Tsai
authors.forename: Casey M
authors.initials: CM
authors.lastname: Bergman
authors.forename: Douda
authors.initials: D
authors.lastname: Bensasson
authors.forename: Michael J T
authors.initials: MJ
authors.lastname: O'Kelly
authors.forename: Alexander
authors.initials: A
authors.lastname: van Oudenaarden
authors.forename: David B H
authors.initials: DB
authors.lastname: Barton
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Bailes
authors.forename: Alex N
authors.initials: AN
authors.lastname: Nguyen
authors.forename: Matthew
authors.initials: M
authors.lastname: Jones
authors.forename: Michael A
authors.initials: MA
authors.lastname: Quail
authors.forename: Ian
authors.initials: I
authors.lastname: Goodhead
authors.forename: Sarah
authors.initials: S
authors.lastname: Sims
authors.forename: Frances
authors.initials: F
authors.lastname: Smith
authors.forename: Anders
authors.initials: A
authors.lastname: Blomberg
authors.forename: Richard
authors.initials: R
authors.lastname: Durbin
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Louis
mesh_terms: D005828:Genetics, Population; D016681:Genome, Fungal / Q000235:genetics*; D023281:Genomics; D005843:Geography; D054643:INDEL Mutation / Q000235:genetics; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012440:Saccharomyces / Q000145:classification / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D012641:Selection, Genetic