Human-mediated selection of yeast cultures has played a huge role in the development of numerous unique strains of Sacchromyces cerevisiae, often attributed to production of a wide variety of wines the world over. Previous studies have indicated a single domesticated origin of S. cerevisiae, termed the “Wine-European” group, but detailed demographic history of the species has been thus far mired by insufficient sampling of wild cultures (especially from oak niches in the Mediterranean) that often coexist with domesticated strains. Almeida et al. (2015) analyze whole genome sequences of 145 strains of S. cerevisiae to understand (a) population genomic structure, and (b) ancestral demography of wild and domestic strains.
Phylogenetic network analyses indicated the positioning of Mediterranean oak strains, and commonly used wine strains in one horizontal extremity, and the other extremity occupied by North American, Asian African, and Caribbean strains, along with six Mediterranean strains. Largely geographical separations of strains were identified at K=10 ancestral subpopulations while using STRUCTURE under an admixture model. Haplotype structure indicated high degrees of shared structure between wine and Mediterranean oak strains, and complex admixture history among all sampled strains, also supported by maximum likelihood phylogenies. Diversity analyses indicate similar levels of polymorphism and diversity in the wine and Mediterranean oak strains, which are both lower than genomic diversity North American, or Asian strains. Demographic analyses of a subset of intronic regions under models of isolation, versus isolation with migration, versus population size growth post isolation using δaδi indicated better fit of the growth model. Estimates of demographic parameters under the growth model showed relatively low migration between strains, a strong bottleneck in the wine strains, with the isolation dated to around 5400-5000 BC, coincident with the first biochemical evidence of wine.
As in the case of crop and livestock domestication, linking wild and domesticated microbe genotypes is an essential step for understanding the roots and trajectories of man-driven artificial selection.
Almeida, Pedro, et al. “A Population Genomics Insight into the Mediterranean Origins of Wine Yeast Domestication.” Molecular Ecology (2015). DOI: 10.1111/mec.13341