New microRNAs in Drosophila--birth, death and cycles of adaptive evolution

PLoS Genet. 2014 Jan;10(1):e1004096. doi: 10.1371/journal.pgen.1004096. Epub 2014 Jan 23.

Abstract

The origin and evolution of new microRNAs (miRNAs) is important because they can impact the transcriptome broadly. As miRNAs can potentially emerge constantly and rapidly, their rates of birth and evolution have been extensively debated. However, most new miRNAs identified appear not to be biologically significant. After an extensive search, we identified 12 new miRNAs that emerged de novo in Drosophila melanogaster in the last 4 million years (Myrs) and have been evolving adaptively. Unexpectedly, even though they are adaptively evolving at birth, more than 94% of such new miRNAs disappear over time. They provide selective advantages, but only for a transient evolutionary period. After 30 Myrs, all surviving miRNAs make the transition from the adaptive phase of rapid evolution to the conservative phase of slow evolution, apparently becoming integrated into the transcriptional network. During this transition, the expression shifts from being tissue-specific, predominantly in testes and larval brain/gonads/imaginal discs, to a broader distribution in many other tissues. Interestingly, a measurable fraction (20-30%) of these conservatively evolving miRNAs experience "evolutionary rejuvenation" and begin to evolve rapidly again. These rejuvenated miRNAs then start another cycle of adaptive - conservative evolution. In conclusion, the selective advantages driving evolution of miRNAs are themselves evolving, and sometimes changing direction, which highlights the regulatory roles of miRNAs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Physiological / genetics*
  • Animals
  • Conserved Sequence
  • Drosophila melanogaster / genetics*
  • Evolution, Molecular*
  • Gene Regulatory Networks
  • MicroRNAs / genetics*

Substances

  • MicroRNAs

Associated data

  • GEO/GSM1165052
  • GEO/GSM1165053
  • GEO/GSM1165054
  • GEO/GSM1165055
  • GEO/GSM1165056

Grants and funding

This work was supported by National Science Foundation of China (31130069, 91231117, 31170308, 41130208, and 31200945), Science Foundation of the State Key Laboratory of Biocontrol (SKLBC10B01 and SKLBC2011A01), and Pearl River Science and Technology Foundation of Guangzhou (2012J2200022). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.