Extensive, Recent Intron Gains in Daphnia Populations

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Science  27 Nov 2009:
Vol. 326, Issue 5957, pp. 1260-1262
DOI: 10.1126/science.1179302

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Inserting Introns

Introns—noncoding regions that interrupt coding gene sequences—are widespread throughout eukaryotic genomes, but intron gains and losses within and among species have been assumed to be rare. However, W. Li et al. (p. 1260) suggest that intron insertions can be relatively frequent within a population or species. By examining intron polymorphisms within genomes of different accessions of Daphnia pulpex (the water flea), and comparisons within the genus Daphnia, several instances of recent intron gains were observed, which appear to have occurred multiple times at the same site. Because intron insertions tend to be flanked by repetitive sequences, they may be the result of DNA damage repair mechanisms.


Rates and mechanisms of intron gain and loss have traditionally been inferred from alignments of highly conserved genes sampled from phylogenetically distant taxa. We report a population-genomic approach that detected 24 discordant intron/exon boundaries between the whole-genome sequences of two Daphnia pulex isolates. Sequencing of presence/absence loci across a collection of D. pulex isolates and outgroup Daphnia species shows that most polymorphisms are a consequence of recent gains, with parallel gains often occurring at the same locations in independent allelic lineages. More than half of the recent gains are associated with short sequence repeats, suggesting an origin via repair of staggered double-strand breaks. By comparing the allele-frequency spectrum of intron-gain alleles with that for derived single-base substitutions, we also provide evidence that newly arisen introns are intrinsically deleterious and tend to accumulate in population-genetic settings where random genetic drift is a relatively strong force.

  • * These authors contributed equally to this work.

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