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Logo of bioldirectBioMed CentralBiomed Central Web Sitesearchsubmit a manuscriptregisterthis articleBiology DirectJournal Front Page
 
Biol Direct. 2012; 7: 36.
Published online Oct 25, 2012. doi:  10.1186/1745-6150-7-36
PMCID: PMC3500645
Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates
Jerzy Jurka,corresponding author1 Weidong Bao,1 Kenji K Kojima,1 Oleksiy Kohany,1 and Matthew G Yurka1
1Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA, 94043, USA
corresponding authorCorresponding author.
Jerzy Jurka: jurka/at/girinst.org; Weidong Bao: weidong/at/girinst.org; Kenji K Kojima: kojima/at/girinst.org; Oleksiy Kohany: kohany/at/girinst.org; Matthew G Yurka: mattyurka/at/gmail.com
Received July 9, 2012; Accepted October 23, 2012.
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.
Reviewers
Eugene Koonin, I. King Jordan, Jürgen Brosius.
Keywords: Transposable elements, Conserved repeats, Genetic drift, Evolution
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