Characterization of newly gained introns in Daphnia populations

Wenli Li, Robert Kuzoff, Chen Khuan Wong, Abraham Tucker, Michael Lynch

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


As one of the few known species in an active phase of intron proliferation, the microcrustacean Daphnia pulex is an especially attractive system for interrogating the gain and loss of introns in natural populations. In this study, we used a comparative populationgenomic approach to identify and characterize 90 recently gained introns in this species. Molecular clock analyses indicate that these introns arose between 3.9 × 105and1.45× 104years ago, with a spike in intron proliferation approximately 5.2 × 104to1.22× 105 years ago. Parallel gains at homologous positions contribute to 47.8% (43/90) of discovered new introns. A disproportionally large number of new introns were found in historically isolated populations in Oregon. Nonetheless, derived, intron-bearing alleles were also identified in a wide range of geographic locations, suggesting intron gain and, to a lesser degree, intron loss are important sources of genetic variation in natural populations of Daphnia. A majority (55/90 or 61.1%) of the identified neointrons have associated internal direct repeats with lengths and compositions that are unlikely to occur by chance, suggesting repeated bouts of staggered double-strand breaks (DSBs) during their evolution. Accordingly, internal, staggered DSBs may contribute to a passive trend toward increased length and sequence diversity in nascent introns.

Original languageEnglish (US)
Pages (from-to)2218-2234
Number of pages17
JournalGenome biology and evolution
Issue number9
StatePublished - Sep 2014
Externally publishedYes


  • Age estimate
  • Daphnia
  • Double-strand breaks
  • New intron

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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