Paper of the week: a critique of ENCODE

This week’s paper of the week is perhaps an add choice for a behavioural ecology lab, but it is relevant for the broader question about the scope of adaptation across genomes and so the reach of natural selection. There has been substantial debate about the extent to which non-coding regions of genomes are influenced by selection, and to what extent they evolve by drift (e.g. the recent book by Mike Lynch for one side of the argument). A key part of this debate is the extent of non-functional, or “junk” DNA in genomes. For many organisms, including humans, junk DNA has been thought to dominate genomes. However, the recent ENCODE project (basically, looking for functional elements in the human genome) has suggested that up to 80% of the genome is “functional” and that the age of “junk DNA” is over. As such, far more of our genome may be under selection than we thought. However, the paper by Dan Graur and colleagues just published in Genome Biology and Evolution demolishes that argument. It is a paper that pulls no punches (and has made mainstream media in the UK, such as a piece in The Observer). The extent to which all those punches hit home can be debated, but it nonetheless challenges very strongly the presentation and associated rhetoric of the ENCODE project (for the lead ENCODE paper go here). The Graur et al critique is especially welcome to me as I have been surprised at the level of scepticism amongst the population genetics community since the ENCODE papers were published; Graur et al provide a way in to the debate (salted with many a pithy comment). Whilst not the last word about the role of natural selection in shaping genome architecture, this paper, and the debate that will no doubt follow, provides a useful corrective.

Graur et al 2013 On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biology and Evolution, in press.

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