The evolutionary importance of gene-expression divergence is unclear: some studies suggest that it is an important mechanism for evolution by natural selection1,2, whereas others claim that most between-species regulatory changes are neutral or nearly neutral3. We examined global transcriptional divergence patterns in a set of Caenorhabditis elegans mutation-accumulation lines and natural isolate lines to provide insights into the evolutionary importance of transcriptional variation and to discriminate between the forces of mutation and natural selection in shaping the evolution of gene expression. We detected the effects of selection on transcriptional divergence patterns and characterized them with respect to coexpressed gene sets, chromosomal clustering of expression changes and functional gene categories. We directly compared observed transcriptional variation patterns in the mutation-accumulation and natural isolate lines to a neutral model of transcriptome evolution to show that strong stabilizing selection dominates the evolution of transcriptional change for thousands of C. elegans expressed sequences.
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We thank K. Duke and M. Jiang for cDNA syntheses and microarray hybridizations and scanning, H. Wu for help with R/MAANOVA, T.D. Kocher for insightful comments and the Caenorhabditis Genetics Center for providing the C. elegans natural isolates. This work was supported by a University of Missouri Research Board grant (to W.K.T.) and US National Institutes of Health grant (to M.L. and W.K.T.). D.R.D. was supported by a US National Institutes of Health National Research Service Award fellowship, and J.T.S. was supported by a postdoctoral fellowship from the Alfred P. Sloan Foundation.
The authors declare no competing financial interests.
Microarray experimental design. (PDF 113 kb)
MA line-specific expression ratios for mount genes. (PDF 1075 kb)
Observed Vg/Vm ratios for gene expression. (PDF 69 kb)
Differentially-expressed genes in the MA lines. (PDF 404 kb)
Differentially-expressed genes in the NI lines. (PDF 97 kb)
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