Fast evolution of core promoters in primate genomes

Han Liang*, Yeong-Shin Lin, Wen Hsiung Li

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


Despite much interest in regulatory evolution, how promoters have evolved remains poorly studied, mainly owing to paucity of data on promoter regions. Using a new set of high-quality experimentally determined core promoters of the human genome, we conducted a comparative analysis of 2,492 human and rhesus macaque promoters and their neighboring nearly neutral regions. We found that the core promoters have an average rate of nucleotide substitution substantially higher than that at 4-fold degenerate sites and only slightly lower than that for the assumed neutral controls of neighboring noncoding regions, suggesting that core promoters are subject to very weak selective constraints. Interestingly, we identified 24 core promoters (at false discovery rate = 50%) that have evolved at an accelerated rate compared with the neutral controls, suggesting that they may have undergone positive selection. The inferred positively selected genes show strong bias in molecular function. We also used population genetic approaches to examine the evolution of core promoters in human populations and found evidence of positive selection at some loci. Taken together, our results suggest that positive selection has played a substantial role in the evolution of transcriptional regulation in primates.

Original languageEnglish
Pages (from-to)1239-1244
Number of pages6
JournalMolecular Biology and Evolution
Issue number6
StatePublished - 1 Jun 2008


  • Hitchhiking
  • Positive selection
  • Primate evolution
  • Regulatory evolution
  • Substitution rate

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