Junk DNA: not quite a scrapyard

I have always been fascinated by junk DNA. I first learned about it as an undergraduate biology student in the early 90s. Junk DNA is "extra" DNA in our genomes, and it doesn’t seem to do much of anything. It doesn’t make protein, which is what DNA is mostly for, it’s not involved in regulating how proteins are made and used (although this is looking less likely), but it does seem to contain occasional degraded (pseudogenes) genes which have lost their functions. In total, I was taught that it is literally useless junk.

This poses an evolutionary problem. Why is 97% of our genome not used? Remember, this is 3,174,022,061 base pairs out of 3,272,187,692 that aren’t being used for anything. Natural selection should quickly eliminate all these extras, since a lot of energy must be wasted on its replication into each cell.

A new study in Nature (subscribers only link) has examined the changes in junk DNA in two fruit fly species, and has found that evolution is definitely affecting the junk regions. What does this mean? Well, it means that although junk DNA goesn’t seem to be doing anything we have yet identified, natural selection is clearly favouring some forms of it. Peter Andolfatto found that in the common laboratory fruit fly, Drosophila melanogaster, the junk DNA regions that don’t make protein are evolving more slowly than regions that do make protein, due to a selection pressure to remain the same.

Then he compared these junk regions that aren’t evolving much with those in a related fruit fly, Drosophila simulans. This time he found a large amount of divergence between the two species’ junk sequences. He says his data show the regions are being subjected to adaptive evolution and purifying selection. Or more simply, natural selection is taking out the trash. Therefore, he says, the junk DNA is performing some kind of function, since selection is operating on these regions in understood ways. Otherwise, random mutations would take over, leading to a slow degradation of these areas of the genome.

Most studies have compared organisms by looking at their protein coding sequences. Now that Andolfatto has shown that junk DNA also varies a lot in non-random ways, it may affect how similarities between species are measured, especially if it someday shown that junk DNA is involved in the regulation and expressions of proteins. “Protein evolution has traditionally been emphasized as a key facet of genome evolution and the evolution of new species,” says Andolfatto in a press release. “The degree of protein sequence similarity between humans and chimpanzees, and other closely-related but morphologically distinct taxa, has prompted several researchers to speculate that most adaptive differences between taxa are due to changes in gene regulation and not protein evolution. My results lend support to this view by demonstrating that regulatory changes have been of great importance in the evolution of new Drosophila species.”

It is important to note that the fruit fly already has a small genome, with 132,576,936 base pairs, and there is not much room for junk, so it is not surprising to find that natural selection is having an effect on it. However, in humans (and onions) the genomes are much larger, and the amount of junk DNA is higher too, and it remains to be seen if something similar is happening in us.

So, to summarize, junk DNA isn’t a scrapyard. If it was, this kind of evolution wouldn’t be happening.