Evolution of Gene Expression


It remains a key challenge in evolutionary biology to learn how variation in genotype within populations of organisms is ultimately associated with adaptive variation in phenotype. Several new molecular and genomic approaches offer promising opportunities to meet this challenge. Among these are DNA microarrays and RNA-seq, which enable expression profiling (genome-wide analysis of the relative abundances of gene transcripts). In principle, these approaches can form a bridge connecting genotype with phenotype, because specific, reproducible patterns of transcription associated with particular genotypes may also be associated with particular phenotypes and affect fitness. Application of expression profiling to natural populations to study the evolution of whole genomes is still in its earliest stages. In our laboratory, we have focused our genomic efforts on the model organisms, yeast and Drosophila.


Previously we provided evidence that sexual selection and sexual differentiation are important in driving the evolution of gene expression networks. For example, among genes that have evolved differences in expression between two Drosophila species that diverged 2.5 million years ago, more than 80% of the differences occur either in one sex only or else involve the gain, loss or reversal of sex-biased expression.


  • Zhou, J., B. Lemos, E. B. Dopman, and D. L. Hartl 2011 Copy number variation: The balance between gene dosage and expression in Drosophila melanogaster. Genome Biol. Evol. 3: 1014-1024.
  • Rogers, R. L., T. Bedford, A. M. Lyons and D. L. Hartl, 2010 Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 107: 10943-10948.
  • Sackton, T. B., R. J. Kulathinal, C. M. Bergman, A. R. Quinlan, E. Dopman, G. T. Marth, M. Carneiro, E. Mardis, , D. L. Hartl and A. G. Clark, 2009 Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biol. Evol. 18: 449-465
  • Fontanillas, P., C. R. Landry, P. J. Wittkopp, C. Russ, J. D. Gruber, and D. L. Hartl, 2010 Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing. Mol. Ecol. 19 (Suppl. 1): 212-227.
  • Bedford, T. and D. L. Hartl, 2009 Optimization of gene expression by natural selection. Proc. Natl. Acad. Sci. USA 106: 1133-1138.
  • Rogers, R. L., T. Bedford and D. L. Hartl, 2009 Formation and longevity of chimeric and duplicate genes in Drosophila melanogaster. Genetics 181: 313–322.
  • Brown, K. M., C. R. Landry, D. L. Hartl, and D. Cavalieri. 2008. Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae. Mol. Ecol. 17: 2985-2997.
  • Landry, C. R., B. Lemos, S. A. Rifkin, W. J. Dickinson, and D. L. Hartl. 2007. Genetic properties influencing the evolvability of gene expression. Science 317: 118-121.
  • Dopman, E. B., and D. L. Hartl. 2007. A portrait of copy-number polymorphism in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 104:19920-19925.
  • Fontanillas, P., D. L. Hartl, and M. Reuter. 2007. Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin. PLoS Genet. 3:e210.
  • Landry, C. R., C. I. Castillo-Davis, A. Ogura, J. S. Liu, and D. L. Hartl. 2007. Systems-level analysis and evolution of the phototransduction network in Drosophila. Proc. Natl. Acad. Sci. USA 104:3283-3288.