Prior posts have noted how in the recent past the perceived wisdom was the 1% of the human genome was responsible for what happens (the making of proteins), and the balance (99%) was "junk." Over time the amount deemed relevant has grown and the junk portion has shrunk. Recently the ENCODE project has concluded that 2/3 of the DNA is being copied into molecules of RNA, which convey protein manufacturing instructions to sub-cellular factories. A nice summary can be found at http://www.nobelprize.org/nobel_prizes/medicine/laureates/1993/illpres/dna-rna.html. What is also interesting is that there may not be a mere 23,000 DNA genes encoding proteins, but millions of mechanisms driven by a species of RNA. The simplistic view of man and (for example) other species having so much in common (or species having much in common genetically with other species) may in fact be flawed, as noted below. Interesting factoid, but not really that relevant, one might say.
Researchers have focused recently on one species of RNA known as lincRNA (long non-coding RNA). See http://en.wikipedia.org/wiki/Long_non-coding_RNA. LincRNA do not encode proteins; more than 9,000 have been identified. Their primary function appears to be to regulate other genes (e.g., attach to DNA switches that control those genes). This is of the same nature as epigenetic modifications, which have been noted in prior posts. [Recall that some epigenetic modifications result, apparently, from lifestyle, which explains (for example) why identical twins are not identical (genetically speaking) as they get older.]
But wait, there's more. lincRNA also contains a second bit of weirdness, transposable elements. See http://en.wikipedia.org/wiki/Transposable_elements. Transposable elements are often called jumping genes" because their DNA can move from one place in the genome to another. [Prior posts have noted that sometimes more than a single gene moves; sometimes it is many, and sometimes they multiple so that where there was one specific gene there is now a string of the samegene. But I digress.] One variety of transposable elements is endogenous retroviruses. These are descendants of ancient diseases that have managed to implant themselves in the genome so that they are passed along like "ordinary" DNA.
Researchers asked: Is not such a movement akin to a mutation, and if so what are its affects? They found some interesting patterns: a) although only 6% of protein encoding genes contain transposable elements, 83% of lincRNA so do; b) the transposable elements in lincRNA are particularly likely to be endogenous retroviruses rather than some other type; c) these transposable elements are usually found where the process of copying RNA from DNA occurs (which indicates that they are involved in switching genes on and off); and, d) lincRNA contain one type of endogenous retrovirus that is quite active in pluripotent stem cells. [See http://www.explorestemcells.co.uk/pluripotentstemcells.html.] This indicates that lincRNA has a role in the arly development of fetuses. lincRNA is also involved in creating various types of tissue; however, each individual lincRNA is active in only one or a few cell types.
Now, we turn to species differentiation. Studies of lincRNA from species as diverse as people, fruit flies, and nematode worms have found they differ more from one species to the next than do protein-encoding genes. Because they are more species specific, they may have an important role to play in differentiating species. Applying ordinary Darwinian mechanics, one would expect most variations created by the movement of transposable elements to be of no consequence or negative (leading to the death of the mutant). But a few may provide some benefit that is passed on through the generations.
So, when we think of speciation and mutations, the focus may have been in the wrong place. We have been looking at protein encoding genes, and not amongst what use to be called the "junk."
The study can be found at: http://genomebiology.com/2012/13/11/R107/abstract. A summary can be found at: http://www.biomedcentral.com/presscenter/pressreleases/20121126a.