Gu, Z. et al. Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 102, 1092-1097

Stanford Genome Technology Center, 855 California Avenue, Palo Alto, CA 94304, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 02/2005; 102(4):1092-7. DOI: 10.1073/pnas.0409159102
Source: PubMed


By using the maximum likelihood method, we made a genome-wide comparison of the evolutionary rates in the lineages leading to the laboratory strain (S288c) and a wild strain (YJM789) of Saccharomyces cerevisiae and found that genes in the laboratory strain tend to evolve faster than in the wild strain. The pattern of elevated evolution suggests that relaxation of selection intensity is the dominant underlying reason, which is consistent with recurrent bottlenecks in the S. cerevisiae laboratory strain population. Supporting this conclusion are the following observations: (i) the increases in nonsynonymous evolutionary rate occur for genes in all functional categories; (ii) most of the synonymous evolutionary rate increases in S288c occur in genes with strong codon usage bias; (iii) genes under stronger negative selection have a larger increase in nonsynonymous evolutionary rate; and (iv) more genes with adaptive evolution were detected in the laboratory strain, but they do not account for the majority of the increased evolution. The present discoveries suggest that experimental and possible industrial manipulations of the laboratory strain of yeast could have had a strong effect on the genetic makeup of this model organism. Furthermore, they imply an evolution of laboratory model organisms away from their wild counterparts, questioning the relevancy of the models especially when extensive laboratory cultivation has occurred. In addition, these results shed light on the evolution of livestock and crop species that have been under human domestication for years.

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    • "In addition to the shuffling of allele frequencies , decrease in population size could lead to the accumulation of slightly deleterious mutations (Ohta 1992). Such an accumulation has been detected by an increase in nonsynonymous (amino acid changing) over synonymous (amino acid conservative) substitutions in dog (Bj€ ornerfeldt et al. 2006; Cruz et al. 2008), laboratory yeast (Gu et al. 2005) and yak (Wang et al. 2011) but also potentially in Asian rice (Lu et al. 2006). Beside demography , other genomic features including recombination rates and genetic linkage to selected sites are known to influence neutral polymorphism levels (Cutter & Payseur 2013). "
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    • "In conclusion, we demonstrate that variation in an important TF is responsible for major phenotypic changes in yeast. Previous studies have highlighted the elevated levels of nonsynonymous changes in TFs among different yeast strains (Gu et al. 2005). Since many human TFs and other regulatory proteins are also polymorphic, it is likely that some of these potential master variators may also be responsible for phenotypic differences, and thus this may be a general mechanism for mediating extensive regulatory (e.g., expression and binding QTLs) and phenotypic variation in all eukaryotes. "
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    • "These strains are often difficult or impossible to sporulate, which suggests that the ability to undergo sexual cycle degenerates in human-made environments (Johnston 1994). An example of a likely joint action of these factors—smaller population size, benign and specific environment, possible adaptation, and asexual reproduction—has been provided by a study in which a laboratory strain of confirmed history of “domestication” was found to undergo an accelerated rate of molecular evolution, demonstrating considerable relaxation of the purifying selection (Gu et al. 2005). "
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