The human genome (like all mammalian genomes) is loaded with sequences that don’t perform any known function. And many of these sequences are junk. And it’s not just mammals — many animal genomes are loaded with junk, as are those of other eukaryotes. That’s not to say that some of the sequences of unknown function do, in fact, have a function that we have yet to identify. However, much of the junk comes from the remnants of transposable element (parasitic sequences that hop around the genome).
That’s not the impression you get from the introduction to a review of transposable elements (TEs) published in the most recent issue of Cell (doi:10.1016/j.cell.2008.09.022):
Following the discovery of transposons in plants and bacteria, the presence of mobile DNA in eukaryotic species gained widespread acceptance. However, the concept of “controlling elements” gave way to disparaging terms such as selfish DNA and “junk DNA.” Nevertheless, the notion of transposable elements as merely molecular parasites, benign at best and powerful mutagens at worst, that hijack cellular mechanisms for their own selfish propagation, seemed incomplete to some biologists. Given that evolution tends to dispose of that which is useless and harmful for a species, it was curious that the genome should be cluttered with so much “junk.” Now we understand that genomes have coevolved with their transposable elements, devising strategies to prevent them from running amok while coopting function from their presence. Repetitive DNA, and retrotransposons in particular, can drive genome evolution and alter gene expression. Evolution has been adept at turning some “junk” into treasure.
I don’t see how the hypothesis that transposons are selfish genetic elements conflicts with the observation that host genomes have coevolved with these parasites. That is, in fact, what we expect to happen between hosts and parasites — red queen and all.
As for cooption, that probably applies to a minority of TEs in eukaryotic genomes. The vast majority of them are just there, incapable of being removed by natural selection. Why? Because selection can only efficiently remove features that are deleterious enough to overcome the effects of genetic drift (the random change in allele frequencies due to sampling error).
Are TEs just hangers on? No, they can dramatically change the architecture of a genome. However, that does not meaning they are being exapted. It just means that they’re there, and that’s what they do. They can lead to the deletion of functional elements. They can rearrange chromosomes. They can even be used to control the expression of nearby genes. That last one is an example of exaptation. The others are merely things that happen as the result of TEs. They can be deleterious, neutral, or beneficial.
But TEs aren’t kept around because they have the potential to do lots of stuff to the host genome. That’s not how natural selection works — it can’t look into the future. The TEs are kept around because the deleterious effects of those mutations (rearrangements, insertions, deletions) aren’t bad enough to cause the TEs to be purged from the genomes in which they reside.
Goodier and Kazazian. 2008. Retrotransposons Revisited: The Restraint and Rehabilitation of Parasites. Cell 135: 23-35 doi:10.1016/j.cell.2008.09.022