title: Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers.
abstract: BACKGROUND
  Sequence analysis of the orangutan genome revealed that recent proliferative activity of Alu elements has been uncharacteristically quiescent in the Pongo (orangutan) lineage, compared with all previously studied primate genomes. With relatively few young polymorphic insertions, the genomic landscape of the orangutan seemed like the ideal place to search for a driver, or source element, of Alu retrotransposition.
  
  
  RESULTS
  Here we report the identification of a nearly pristine insertion possessing all the known putative hallmarks of a retrotranspositionally competent Alu element. It is located in an intronic sequence of the DGKB gene on chromosome 7 and is highly conserved in Hominidae (the great apes), but absent from Hylobatidae (gibbon and siamang). We provide evidence for the evolution of a lineage-specific subfamily of this shared Alu insertion in orangutans and possibly the lineage leading to humans. In the orangutan genome, this insertion contains three orangutan-specific diagnostic mutations which are characteristic of the youngest polymorphic Alu subfamily, AluYe5b5_Pongo. In the Homininae lineage (human, chimpanzee and gorilla), this insertion has acquired three different mutations which are also found in a single human-specific Alu insertion.
  
  
  CONCLUSIONS
  This seemingly stealth-like amplification, ongoing at a very low rate over millions of years of evolution, suggests that this shared insertion may represent an ancient backseat driver of Alu element expansion.
authors.affiliation: Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.
authors.forename: Jerilyn A
authors.initials: JA
authors.lastname: Walker
authors.affiliation: Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.
authors.forename: Miriam K
authors.initials: MK
authors.lastname: Konkel
authors.affiliation: Department of Computer Science, Center for Computation and Technology (CCT), Louisiana State University, 316 Johnston Hall, Baton Rouge, LA 70803, USA.
authors.forename: Brygg
authors.initials: B
authors.lastname: Ullmer
authors.affiliation: Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.|Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130, USA.|School of Biological Sciences, Louisiana Tech University, Ruston, LA 71272, USA.
authors.forename: Christopher P
authors.initials: CP
authors.lastname: Monceaux
authors.affiliation: Conservation and Research for Endangered Species (CRES), Zoological Society of San Diego, San Diego, CA 92112, USA.
authors.forename: Oliver A
authors.initials: OA
authors.lastname: Ryder
authors.affiliation: Institute for Systems Biology, Seattle, WA 98103, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Hubley
authors.affiliation: Institute for Systems Biology, Seattle, WA 98103, USA.
authors.forename: Arian Fa
authors.initials: AF
authors.lastname: Smit
authors.affiliation: Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Batzer