Its no secret that repeat DNA makes up the majority of the genome in a majority of "higher" eukaryotes. For a long time this repeat DNA has been considered "selfish" or "parasitic" DNA, its only feature was its prolific self-propagation as it hitchhiked a ride throughout evolutionary history at the energetic expense of the host.
Nina Fedoroff argues in a recent review in Science that these transposable elements are not "junk" at all, and in fact they play "a profoundly generative role in genome evolution" where the transposons provide novel mechanisms to generate genetic diversity. Nina explores the relationship between genome size and epigenetic complexity in the comparison of eukaryotes and prokaryotes, postulating that the innovation of epigenetic elaborate control mechanisms in bacteria paved the way for increases in genome size and complexity we see in eukaryotes. So rather than epigenetic mechanisms evolving to keep "parasitic DNA" in check, it was these epigenetic mechanisms precisely which actually silenced them just enough to make them tolerable in the genome where, on occasion they provide spontaneous recombination activity, giving rise to bursts of increasing genome size, occasionally providing bursts of fitness. Transposase activity is proposed to give species an adaptive advantage in the long term, assisting in the speed of genome evolution. It makes sense that these "copy-and-paste" tools have a beneficial effect on the genome on evolutionary scales, otherwise we probably wouldn't be carrying such a humongous variety and amount of them!
Science. 2012 Nov 9;338(6108):758-67.
Presidential address. Transposable elements, epigenetics, and genome evolution.
King Abdullah University of Science and Technology, Saudi Arabia. firstname.lastname@example.org
PMID: 23145453 [PubMed - in process]