title: Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates.
abstract: BACKGROUND
  Mammalian genomes are repositories of repetitive DNA sequences derived from transposable elements (TEs). Typically, TEs generate multiple, mostly inactive copies of themselves, commonly known as repetitive families or families of repeats. Recently, we proposed that families of TEs originate in small populations by genetic drift and that the origin of small subpopulations from larger populations can be fueled by biological innovations.
  
  
  RESULTS
  We report three distinct groups of repetitive families preserved in the human genome that expanded and declined during the three previously described periods of regulatory innovations in vertebrate genomes. The first group originated prior to the evolutionary separation of the mammalian and bird lineages and the second one during subsequent diversification of the mammalian lineages prior to the origin of eutherian lineages. The third group of families is primate-specific.
  
  
  CONCLUSIONS
  The observed correlation implies a relationship between regulatory innovations and the origin of repetitive families. Consistent with our previous hypothesis, it is proposed that regulatory innovations fueled the origin of new subpopulations in which new repetitive families became fixed by genetic drift.
authors.affiliation: Genetic Information Research Institute, Mountain View, CA 94043, USA. jurka@girinst.org
authors.forename: Jerzy
authors.initials: J
authors.lastname: Jurka
authors.forename: Weidong
authors.initials: W
authors.lastname: Bao
authors.forename: Kenji K
authors.initials: KK
authors.lastname: Kojima
authors.forename: Oleksiy
authors.initials: O
authors.lastname: Kohany
authors.forename: Matthew G
authors.initials: MG
authors.lastname: Yurka
mesh_terms: D000818:Animals; D001717:Birds / Q000235:genetics; D016384:Consensus Sequence; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D016678:Genome; D015894:Genome, Human; D006801:Humans; D020071:Interspersed Repetitive Sequences; D008322:Mammals / Q000235:genetics*; D011323:Primates / Q000235:genetics; D017422:Sequence Analysis, DNA; D014714:Vertebrates / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements