Not a Living Fossil: How a Prehistoric Ocean Predator Became a New Creature Genetically

The ancient fish once thought extinct picked up 62 new genes 10 million years ago, leading scientists to wonder where they came from.

Coelacanth off Pumula on the KwaZulu-Natal South Coast, South Africa, in November 2019. (Bruce A.S. Henderson, Michael D. Frazer, et al. / South African Journal of Science)

(CN) — The coelacanth, a fish that scientists once thought extinct for 65 million years, had more surprises in store as researchers discovered the modern-day species picked up 62 new genes throughout its long, mysterious history.

Dubbed a “living fossil” when it was captured off the coast of South Africa in 1938 because it looked anatomically identical to its fossil record, the mighty ocean predator coelacanth had another surprise in store.

In a study published Tuesday in the journal Molecular Biology and Evolution, scientists detailed how the African coelacanth picked up new genetic material through its interactions with other fish approximately 10 million years ago. So while its body has changed very little in 65 million years, genetically it’s a different creature.

The researchers found that the genes were gained from transposons, parasitic DNA sequences that only make copies of themselves, sometimes by moving between different species.

“Our findings provide a rather striking example of this phenomenon of transposons contributing to the host genome,” said Tim Hughes, senior study author and professor of molecular genetics in the Donnelly Centre for Cellular and Biomolecular Research at the University of Toronto in Canada.

“We don’t know what these 62 genes are doing, but many of them encode DNA binding proteins and probably have a role in gene regulation, where even subtle changes are important in evolution,” Hughes added.

Also called “jumping genes,” transposons are able to switch locations in the genome due to an enzyme that moves its own DNA via what the researchers call a “cut and paste” mechanism.

“New copies can arise through serendipitous jumps during cell division when the whole genome is replicated. Over time, the enzyme’s code drifts into disrepair and the jumping ceases. But if the altered sequence confers even subtle selective advantage to the host, it can begin new life as a bona fide host gene,” the researchers said in a statement.

“It was surprising to see coelacanths pop out among vertebrates as having a really large number of these transposon-derived genes because they have an undeserved reputation of being a living fossil,” said graduate student Isaac Yellan who led the study. “The coelacanth may have evolved a bit more slowly, but it is certainly not a fossil.”

Yellan said he discovered the genes while looking for evidence of a counterpart of a human gene in other species. He found that the transposons were carried between species at different times through what scientists call a horizontal gene transfer. 

“Horizontal gene transfer fuzzies up the picture of where the transposons came from, but we know from other species that it can occur via parasitism,” Yellan said. “The most likely explanation is that they were introduced multiple times throughout evolutionary history.”

The researchers said they don’t know yet the purpose of the new genes, but evidence suggests they play a part in gene regulation. They added it may be impossible to figure out where the genes came from due to the elusiveness of the fish.

“The coelacanths are extremely rare,” Yellan said. “And they’re very good at hiding.”

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