Abstract
Interactions between an organism and its environment can significantly influence phenotypic evolution. A first step toward understanding this process is to characterize phenotypic diversity within and between populations. We explored the phenotypic variation in stress sensitivity and genomic expression in a large panel of Saccharomyces strains collected from diverse environments. We measured the sensitivity of 52 strains to 14 environmental conditions, compared genomic expression in 18 strains, and identified gene copy-number variations in six of these isolates. Our results demonstrate a large degree of phenotypic variation in stress sensitivity and gene expression. Analysis of these datasets reveals relationships between strains from similar niches, suggests common and unique features of yeast habitats, and implicates genes whose variable expression is linked to stress resistance. Using a simple metric to suggest cases of selection, we found that strains collected from oak exudates are phenotypically more similar than expected based on their genetic diversity, while sake and vineyard isolates display more diverse phenotypes than expected under a neutral model. We also show that the laboratory strain S288c is phenotypically distinct from all of the other strains studied here, in terms of stress sensitivity, gene expression, Ty copy number, mitochondrial content, and gene-dosage control. These results highlight the value of understanding the genetic basis of phenotypic variation and raise caution about using laboratory strains for comparative genomics.
Highlights
A major focus of genetic study is to elucidate the effects of genetic variation on phenotypic diversity
A major focus of study is defining the genetic basis for phenotypes important for organismal fitness
As a first step toward this goal, we surveyed phenotypic variation in diverse yeast strains collected from different environments by characterizing variations in stress resistance and genomic expression
Summary
A major focus of genetic study is to elucidate the effects of genetic variation on phenotypic diversity. The evolution of phenotypes is often driven by environmental factors and the interactions between each organism and its environment. There has been a renewed interest in characterizing the diversity and ecology of organisms long used in the laboratory as models for biological study. Worms, flies, and mice have been studied on a molecular level for decades and have provided many insights into basic biology. Most of our knowledge base exists for only a handful of domesticated lines. Little is known about the natural ecology of these organisms or the degree to which individuals of each species vary within and between natural populations
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