The genomic basis of circadian and circalunar timing adaptations in a midge

Nature. 2016 Dec 1;540(7631):69-73. doi: 10.1038/nature20151. Epub 2016 Nov 21.


Organisms use endogenous clocks to anticipate regular environmental cycles, such as days and tides. Natural variants resulting in differently timed behaviour or physiology, known as chronotypes in humans, have not been well characterized at the molecular level. We sequenced the genome of Clunio marinus, a marine midge whose reproduction is timed by circadian and circalunar clocks. Midges from different locations show strain-specific genetic timing adaptations. We examined genetic variation in five C. marinus strains from different locations and mapped quantitative trait loci for circalunar and circadian chronotypes. The region most strongly associated with circadian chronotypes generates strain-specific differences in the abundance of calcium/calmodulin-dependent kinase II.1 (CaMKII.1) splice variants. As equivalent variants were shown to alter CaMKII activity in Drosophila melanogaster, and C. marinus (Cma)-CaMKII.1 increases the transcriptional activity of the dimer of the circadian proteins Cma-CLOCK and Cma-CYCLE, we suggest that modulation of alternative splicing is a mechanism for natural adaptation in circadian timing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acclimatization / genetics*
  • Alternative Splicing / genetics
  • Animals
  • CLOCK Proteins / genetics
  • Calcium-Calmodulin-Dependent Protein Kinase Type 2 / genetics
  • Calcium-Calmodulin-Dependent Protein Kinase Type 2 / metabolism
  • Chironomidae / classification
  • Chironomidae / genetics*
  • Chironomidae / physiology
  • Circadian Clocks / genetics*
  • Circadian Rhythm / genetics*
  • Drosophila melanogaster / enzymology
  • Drosophila melanogaster / genetics
  • Genetic Association Studies
  • Genetic Variation
  • Genome, Insect / genetics*
  • Genomics*
  • Male
  • Moon
  • Phenotype
  • Quantitative Trait Loci / genetics
  • Reproduction / genetics
  • Reproduction / physiology
  • Species Specificity
  • Tidal Waves*
  • Time Factors
  • Transcription, Genetic


  • CLOCK Proteins
  • Calcium-Calmodulin-Dependent Protein Kinase Type 2