title: Characterization of newly gained introns in Daphnia populations.
abstract: 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 population-genomic approach to identify and characterize 90 recently gained introns in this species. Molecular clock analyses indicate that these introns arose between 3.9 × 10(5) and 1.45 × 10(4) years ago, with a spike in intron proliferation approximately 5.2 × 10(4) to 1.22 × 10(5) 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.
authors.affiliation: Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin wenli@mcw.edu.
authors.forename: Wenli
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Biology, University of Wisconsin-Whitewater.
authors.forename: Robert
authors.initials: R
authors.lastname: Kuzoff
authors.affiliation: Genetics and Genomics Program, Department of Medicine, Boston University.
authors.forename: Chen Khuan
authors.initials: CK
authors.lastname: Wong
authors.affiliation: Department of Biology, Southern Arkansas University.
authors.forename: Abraham
authors.initials: A
authors.lastname: Tucker
authors.affiliation: Department of Biology, Indiana University, Bloomington.
authors.forename: Michael
authors.initials: M
authors.lastname: Lynch
mesh_terms: D000483:Alleles; D000818:Animals; D001483:Base Sequence; D003621:Daphnia / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D014644:Genetic Variation; D016678:Genome; D007438:Introns; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny
keywords: Daphnia; age estimate; double-strand breaks; new intron