  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 (known as 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 mixtures of alleles from European and Asian
populations, indicating an admixed origin for this group. In the context of
this global diversity, we demonstrate that a collection of seven strains
commonly used in the laboratory encompasses only one quarter of the genetic
diversity present in the full collection of strains, underscoring the
relatively limited genetic diversity captured by the current set of lab
strains. 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.
