title: Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq.
abstract: The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for a number of fields, including genetics, bioengineering, and studies of evolution and population structure. Here, we apply a multiplexed, reduced genome sequencing strategy (restriction site-associated sequencing or RAD-seq) to genotype a large collection of S. cerevisiae strains isolated from a wide range of geographical locations and environmental niches. The method permits the sequencing of the same 1% of all genomes, producing a multiple sequence alignment of 116,880 bases across 262 strains. We find diversity among these strains is principally organized by geography, with European, North American, Asian, and African/S. E. Asian populations defining the major axes of genetic variation. At a finer scale, small groups of strains from cacao, olives, and sake are defined by unique variants not present in other strains. One population, containing strains from a variety of fermentations, exhibits high levels of heterozygosity and a mixture of alleles from European and Asian populations, indicating an admixed origin for this group. We propose a model of geographic differentiation followed by human-associated admixture, primarily between European and Asian populations and more recently between European and North American populations. The large collection of genotyped yeast strains characterized here will provide a useful resource for the broad community of yeast researchers.
authors.affiliation: Institute for Systems Biology, Seattle, Washington 98109.
authors.forename: Gareth A
authors.initials: GA
authors.lastname: Cromie
authors.forename: Katie E
authors.initials: KE
authors.lastname: Hyma
authors.forename: Catherine L
authors.initials: CL
authors.lastname: Ludlow
authors.forename: Cecilia
authors.initials: C
authors.lastname: Garmendia-Torres
authors.forename: Teresa L
authors.initials: TL
authors.lastname: Gilbert
authors.forename: Patrick
authors.initials: P
authors.lastname: May
authors.forename: Angela A
authors.initials: AA
authors.lastname: Huang
authors.forename: Aimée M
authors.initials: AM
authors.lastname: Dudley
authors.forename: Justin C
authors.initials: JC
authors.lastname: Fay
mesh_terms: D014644:Genetic Variation; D005828:Genetics, Population; D016681:Genome, Fungal; D006579:Heterozygote; D058974:Phylogeography; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: RAD-seq; genetic diversity; phylogenetics; population structure; yeast