Intron presence-absence polymorphisms in Daphnia

Angela R. Omilian, Douglas G. Scofield, Michael Lynch

Research output: Contribution to journalArticlepeer-review

34 Scopus citations


Here, we report 2 novel intron gains segregating in populations of Daphnia pulex endemic to Oregon. These novel introns do not have an obvious source and are not present in any D. pulex populations outside Oregon, other species of Daphnia that we examined, or any other organism for which sequence data are available. Furthermore, the novel introns are both found in the same gene, a Rab GTPase (rab4), and they appear to differ in their insertion site by one base pair, providing some support to the proto-splice site hypothesis. The rarity of intron-gain polymorphisms is questioned as we discovered 2 events in an initial survey of only 6 nuclear loci in 36 Daphnia individuals. Neutrality tests failed to ascertain a clear selective effect for either intron insertion, and a significant difference in recombination rate was not observed in alleles that contain the novel intron insertion versus alleles lacking it. We conclude that one novel intron insertion segregating at high frequencies in Daphnia populations in Oregon is unlikely to be adaptive and may result from the reduced efficacy of selection in isolated populations of small effective size.

Original languageEnglish (US)
Pages (from-to)2129-2139
Number of pages11
JournalMolecular biology and evolution
Issue number10
StatePublished - Oct 2008
Externally publishedYes


  • Daphnia
  • Intron gain
  • Intron insertion
  • Intron polymorphism

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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