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Intra- and inter-specific variations of gene expression levels in yeast are largely neutral

Jian-Rong Yang, Calum Maclean, Chungoo Park, Huabin Zhao, Jianzhi Zhang
doi: https://doi.org/10.1101/089995
Jian-Rong Yang
1Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Calum Maclean
1Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Chungoo Park
1Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Huabin Zhao
1Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Jianzhi Zhang
1Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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  • For correspondence: jianzhi@umich.edu
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ABSTRACT

It is commonly, although not universally, accepted that most intra- and inter-specific genome sequence variations are more or less neutral, whereas a large fraction of organism-level phenotypic variations are adaptive. Gene expression levels are molecular phenotypes that bridge the gap between genotypes and corresponding organism-level phenotypes. Yet, it is unknown whether natural variations in gene expression levels are mostly neutral or adaptive. Here we address this fundamental question by genome-wide profiling and comparison of gene expression levels in nine yeast strains belonging to three closely related Saccharomyces species and originating from five different ecological environments. We find that the transcriptome-based clustering of the nine strains approximates the genome sequence-based phylogeny irrespective of their ecological environments. Remarkably, only ∼0.5% of genes exhibit similar expression levels among strains from a common ecological environment, no greater than that among strains with comparable phylogenetic relationships but different environments. These and other observations strongly suggest that most intra- and inter-specific variations in yeast gene expression levels result from the accumulation of random mutations rather than environmental adaptations. This finding has profound implications for understanding the driving force of gene expression evolution, genetic basis of phenotypic adaptation, and general role of stochasticity in evolution.

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Posted November 28, 2016.
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Intra- and inter-specific variations of gene expression levels in yeast are largely neutral
Jian-Rong Yang, Calum Maclean, Chungoo Park, Huabin Zhao, Jianzhi Zhang
bioRxiv 089995; doi: https://doi.org/10.1101/089995
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Intra- and inter-specific variations of gene expression levels in yeast are largely neutral
Jian-Rong Yang, Calum Maclean, Chungoo Park, Huabin Zhao, Jianzhi Zhang
bioRxiv 089995; doi: https://doi.org/10.1101/089995

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