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Dark DNA: The Latest Enigma in the Field of Genetics

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No doubt we all have heard of dark matter, which is thought to make up over a quarter of the universe. We know it’s there; we just haven’t been able to detect it. Well, something similar phenomena occur in the genome [1]. DNA sequencing technology is helping scientists unravel questions that humans have been asking about animals for centuries. By mapping out animal genomes, we now have a better idea of how the giraffe got its huge neck and why snakes are so long. Genome sequencing allows us to compare and contrast the DNA of different animals and work out how they evolved in their unique ways [2].

But in some cases, scientists are faced with a mystery of missing genes. Some animal genomes seem to be missing certain genes, ones that appear in other similar species, and must be present to keep the animals alive. These apparently missing genes have been dubbed “Dark DNA”. And its existence could change the way we think about evolution [2]. The sand rat (Psammomys obesus) is a desert species native to North Africa and the Middle East, but put it in a lab and something strange happens. When fed a “normal” diet – the standard fare for laboratory rodents – sand rats tend to become obese and develop type 2 diabetes. This was discovered in the 1960s and has made sand rats the focus of study for biologists interested in understanding nutrition-induced diabetes in humans. Yet, in all that time, the mystery of why these gerbils are so susceptible to type 2 diabetes remained.

Finally, a group of scientists solved this puzzle. When they looked for a gene called Pdx1 that controls the secretion of insulin, they found it was missing, as were 87 other genes surrounding it. Some of these missing genes, including Pdx1, are essential and without them, an animal cannot survive. So where are they? The first clue was that, in several of the sand rat’s body tissues, we found the chemical products that the instructions from the “missing” genes would create. This would only be possible if the genes were present somewhere in the genome, indicating that they weren’t really missing but just hidden [3].

By studying the sand rat genome further, the scientists found that one part of it, in particular, had many more mutations than are found in other rodent genomes. All the genes within this mutation hotspot now have very GC-rich DNA and have mutated to such a degree that they are hard to detect using standard methods. Excessive mutation will often stop a gene from working, yet somehow the sand rat’s genes manage to still fulfill their roles despite radical change to the DNA sequence. This is a very difficult task for genes. It’s like winning Countdown using only vowels.

This kind of dark DNA has previously been found in birds. Scientists have found that 274 genes are “missing” from currently sequenced bird genomes. These include the gene for leptin (a hormone that regulates energy balance), which scientists have been unable to find for many years. Once again, these genes have a very high GC content and their products are found in the birds’ body tissues, even though the genes appear to be missing from the genome sequences.

Shedding light on dark DNA

Most textbook definitions of evolution state that it occurs in two stages: mutation followed by natural selection. DNA mutation is a common and continuous process and occurs completely at random. Natural selection then acts to determine whether mutations are kept and passed on or not, usually depending on whether they result in higher reproductive success. In short, mutation creates the variation in an organism’s DNA, natural selection decides whether it stays or if it goes, and so biases the direction of evolution [2].

But hotspots of high mutation within a genome mean genes in certain locations have a higher chance of mutating than others. This means that such hotspots could be an underappreciated mechanism that could also bias the direction of evolution, meaning natural selection may not be the sole driving force. Hargreaves and colleagues [3] believe the desert rat may have undergone a fast evolutionary jump, which is why the hotspot occurred. Today, human-driven climate change is speeding up evolutionary processes among many species. More cases of dark DNA could be one result [4].

So far, dark DNA seems to be present in two very diverse and distinct types of animals. But it’s still not clear how widespread it could be. Could all animal genomes contain dark DNA and, if not, what makes gerbils and birds so unique? The most exciting puzzle to solve will be working out what effect dark DNA has had on animal evolution.



  1. Dark DNA: The missing matter at the heart of nature.
  2. Hargreaves A D. Introducing ‘dark DNA’ – the phenomenon that could change how we think about evolution.
  3. Hargreaves A D, Zhou L, Christensen J et al. Genome sequence of a diabetes-prone rodent reveals a mutation hotspot around the ParaHox gene cluster. PNAS 2017; 114 (29) 7677-7682.
  4. Perry P. “Dark DNA” is changing the way we see evolution.

Dr. Sanjoy Kumar Pal is a Professor of Biology in Skyline University Nigeria. He has a PhD. in Animal Genetics from Indian Veterinary Research Institute.

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