What We Talk About When We Talk About "Junk DNA"

Abstract

"Junk DNA" is a popular yet controversial concept that states that organisms carry in their genomes DNA that has no positive impact on their fitness. Nonetheless, biochemical functions have been identified for an increasing fraction of DNA elements traditionally seen as "Junk DNA". These findings have been interpreted as fundamentally undermining the "Junk DNA" concept. Here, we reinforce previous arguments that this interpretation relies on an inadequate concept of biological function that does not consider the selected effect of a given genomic structure, which is central to the "Junk DNA" concept. Next, we suggest that another (though ignored) confounding factor is that the discussion about biological functions includes two different dimensions: a horizontal, ecological dimension that reflects how a given genomic element affects fitness in a specific time, and a vertical, temporal dimension that reflects how a given genomic element persisted along time. We suggest that "Junk DNA" should be used exclusively relative to the horizontal dimension, while for the vertical dimension, we propose a new term, "Spam DNA", that reflects the fact that a given genomic element may persist in the genome even if not selected for on their origin. Importantly, these concepts are complementary. An element can be both "Spam DNA" and "Junk DNA", and "Spam DNA" can also be recruited to perform evolved biological functions, as illustrated in processes of exaptation or constructive neutral evolution.

Keywords: biological function; exaptation; genome evolution; positive selection; purifying selection; spam DNA.

Fig. 1.

The horizontal and vertical dimensions in genome evolution, and the possible fates of new genomic elements. The vertical dimension can be thought of as a succession of (horizontal) time slices where the ecological relations are always changing. Depending on the impact of selection, a new genomic element can originate as “Functional” (green polygons) or “Junk” (red crosses) in a specific time slice. Along different time slices, “Junk” elements may be converted into “Functional” ones (if they acquire “maintenance functions”) and vice-versa (if they are no longer maintained by selection). On the other hand, “Spam DNA”, highlighted in the blue shade, depends on neutral processes causing the persistence of this element along the time, irrespective of their future function.