The coelacanth, a powerful ocean predator, was first caught alive in 1938 off the coast of South Africa. The find caused quite a stir, as it was believed to be extinct 65 million years ago. The fish was popularly recognized as a “living fossil”, as its anatomy was almost identical to that of the fossil record. It recalls a prehistoric fish stopped in evolution, which seems about to change its fins for legs and fingers. But while the coelacanth’s body may have changed little, its genome, deciphered by an international team in 2013, tells a different story.
Canadian scientists have discovered that the African coelacanth, (Latimeria chalumnae) gained 62 new genes through encounters with other species 10 million years ago. Their findings are published in the journal “Molecular Biology and Evolution.” The researchers believe that these genes arose from transposons, also known as “selfish genes.” These are parasitic DNA elements whose sole purpose is to make more copies of themselves, which they sometimes accomplish by moving between species.
“It’s a pretty amazing example of this phenomenon of transposons contributing to the host genome,” says Tim Hughes, lead author of the study and professor of molecular genetics at the Donnelly Center for Cellular and Biomolecular Research at the University of Toronto. “We don’t know what these 62 genes are doing, but many of them code for DNA-binding proteins and probably have a role in gene regulation, where even subtle changes are important in evolution,” he explains.
Transposons are also called “jumping genes” because they change their location in the genome, thanks to a self-encoded enzyme that recognizes and moves its DNA code through the “cut and paste” mechanism. New copies can arise through random jumps during cell division when the entire genome is replicated.
Over time, the enzyme code deteriorates and the jump stops. But if the altered sequence confers even a subtle selective advantage on the host, it can begin a new life as a genuine host gene. There are countless examples of transposon-derived genes in all species, but the coelacanth stands out for its large scale.
“It was surprising to see coelacanths show up among vertebrates for having a large number of these transposon-derived genes because they have an undeserved reputation for being a living fossil,” says Isaac Yellen, who led the study. “The coelacanth may have evolved a little more slowly, but it is certainly not a fossil,” he stresses.
Yellen discovered while looking for counterparts in other species of a human gene she was studying. He knew that the gene, CGGBP1, had arisen from a particular type of transposon in the common ancestor of mammals, birds, and reptiles. After scanning all the available genomes, Yellen was able to find related genes, but their distribution between species was patchy and not what you would expect from a common ancestor. In addition to the unique CGGBP-like gene in all mammals, birds, and reptiles, Yellen found copies in some, but not all, of the fish he observed, as well as in the lamprey, a primitive vertebrate and type of fungus. Worms, mollusks, and most insects had none. And then 62 appeared on the coelacanth.
With common ancestry ruled out, it appears instead that the transposons reached various lineages at different times by being transported between species through what is known as horizontal gene transfer. “Horizontal gene transfer blurs the picture of where transposons come from, but we know from other species that it can occur through parasitism,” Yellen says. “The most likely explanation is that they were introduced multiple times throughout evolutionary history.”
It’s unclear what the genes are doing, but several lines of evidence point to a role in gene regulation. Computational modeling and test-tube experiments established that gene products are proteins that bind unique sequence signatures in DNA, suggesting a role in gene expression, similar to the human counterpart. Furthermore, genes are variably turned on in a dozen coelacanth organs for which data exist, suggesting finely tuned functions that are tissue-specific.
The origin of the genes and what they are doing in the coelacanth may remain a mystery. Research specimens are only occasionally taken by fishing boats and it was not until 1998 that the other known living species, Latimeria menadoensis, was discovered in an Indonesian fish market.
The species divided before the new genes appeared, ruling them out of driving speciation. Even so, they could have shaped the African coelacanth we know today, whose majestic blue-scaled armor casts a shadow over its brown relative, although Yellen points out that this is pure speculation. Unfortunately, he acknowledges, we may never know, as coelacanths “are extremely rare and very good at hiding.