In 1938, a living relic, thought to be extinct 65 million years ago, was accidentally caught in a trawl net off the coast of South Africa.
The 2 meter long coelacanth (Latimeria chalumnae) turned out to be one of our closest fish relatives – looking largely unchanged since the most recent appearance in the fossil record from the days of non-avian dinosaurs.
Now, new genetic evidence shows that this deep-sea predator has undergone a hidden, but widespread, evolution at the genetic level – by hijacking genes from other species.
While searching genetic databases for the ancestral version of a human gene involved in gene regulation, CGGBP1, molecular geneticist Isaac Yellan of the University of Toronto unexpectedly discovered that coelacanth has many variations of this gene.
More unusually, these different variations of the CGGBP genes did not all share a common ancestor. This suggests that at some points, about 10 million years ago, 62 of these genes were wiped out by the coelacanth of other, unrelated species – through horizontal gene transfer.
These genes, with their ability to ‘jump’ around and even between genomes, much like viruses, are known as transposons.
If they happen to jump in the right place in the genome, cellular machinery will copy them just like any other gene. But they can also jump in the wrong place where they can be harmful and thus considered parasitic.
Occasionally, however, they may end up in a position useful to their host species and eventually lose their ability to jump around, but are conserved in their new place in the genome, which appears to have happened multiple times in the coelacanth. .
“Horizontal gene transfer clouds the picture of where the transposons came from, but we know from other species that it can happen through parasitism,” Yellan said. “The most likely explanation is that they have been introduced several times in evolutionary history.”
While it is common to find such transposons among many species, it is uncommon to find so many.
Test-tube experiments and computer modeling showed that at least eight of the proteins these genes encode bind to different repeated sequences of DNA, suggesting that – like the human version – they are involved in gene regulation. Some of them are only expressed in specific tissues.
“We don’t know what these 62 genes do, but many of them code for DNA-binding proteins and probably play a role in gene regulation, with even subtle changes being important in evolution,” explains molecular geneticist Tim Hughes at the University of Toronto.
Coelacanth has leg-like lobed fins and is more closely related to us and our closest fish relatives, the lungfish, than other types of fish. Our very distant shared ancestor means that the coelacanth’s genome has the potential to help us unravel many mysteries about our own evolution.
Unfortunately, these fish are rarely seen and endangered, so the opportunities to study them are limited. But the information we have from them is already proving fruitful.
A recent study of their genes suggests that our bitter receptors may play a role that doesn’t protect us from toxins, such as metabolic regulation and hormone sensing. Now, coelacanth genes have shown that transposons may play a bigger role than we realize in tetrapod evolution.
“Our findings are quite a striking example of this phenomenon of transposons contributing to the host genome,” said Hughe.
This research is published in Molecular Biology and Evolution.