African coelacanth fish evolved dozens of new genes just 10 million years ago

Feb. 9 (UPI) — When the first living African coelacanth fish, sometimes called the gombessa, was caught in 1938, researchers were stunned. They thought the fish had been extinct for 65 million years.

Scientists were even more surprised to find the species looked almost exactly the same as its earliest relatives. They called the fish a “living fossil.”

Fast forward more than 80 years, and scientists have now shown the species, Latimeria chalumnae, did not spend the last 65 million years in evolutionary stasis.

According to a new paper, published Tuesday in the journal Molecular Biology and Evolution, the ocean predator acquired 62 new genes around 10 million years ago.

Sequencing data suggests the novel genes were forged by transposons, DNA sequences known as selfish genes. These traveling DNA sequences, also called jumping genes, can alter their position within the genome — moving, replicating and rearranging themselves.

Scientists suspect the African coelacanth fish acquired a variety of transposons via interactions with other species. Selfish genes regularly jump from one species to another.

“Our findings provide a rather striking example of this phenomenon of transposons contributing to the host genome,” senior study author Tim Hughes said in a news release.

“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,” said Hughes, a professor of molecular genetics at the University of Toronto.

Transposons boast a self-encoded enzyme that allows these traveling sequences to recognize, copy, relocate and paste its DNA coding into a new part of the genome. The cell division process, during which the genome is replicated, ensures these sequences are spread across the genome.

Over time, jumping gene sequences become broken and their ability to replicate and relocate is lost. However, if these selfish genes happen to offer the host organism a competitive advantage, they can become cemented in a species genome.

Functional transposon-derived genes have been found in a variety of species, but scientists were surprised to find so many in a species many scientists considered to be frozen in evolutionary time.

“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 lead study author Isaac Yellan.

“The coelacanth may have evolved a bit more slowly but it is certainly not a fossil,” said Yellan, a graduate student at the University of Toronto.

Yellan discovered the concentration of transposon-related genes in the African coelacanth fish while searching for corollaries of a human gene called CGGBP1.

The transposon-derived gene first evolved in a common ancestor of mammals, birds and reptiles. Despite its ancient origins, Yellan struggled to find counterparts in other commonly studied species.

Using genomic databases, he found isolated instances of CGGBP-related genes in an odd assortment of mammals, reptiles and birds. He also found examples of CGGBP-like genes in a lamprey, a primitive vertebrate and a rare fungus.

Eventually, his survey brought him to Latimeria chalumnae. The African coelacanth fish’s genome, which was sequenced and added to genomic databases for the first time in 2013, boasted 62 CGGBP-like genes.

Researchers determined all those transposon-related genes were unlikely to have derived from a single common ancestor. Instead, the CGGBP-like genes most likely followed a variety of lineages, arriving at different times via 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,” said Yellan. “The most likely explanation is that they were introduced multiple times throughout evolutionary history.”

Test tube experiments and computer models suggest the CGGBP-like genes found in the coelacanth’s genome produce proteins that help bind specific sequences to DNA, which alters how genetic coding gets transcribed and expressed.

The research suggests CGGBP-like genes in coelacanth fish likely play a sophisticated role in gene expression, similar to the role CGGBP1 plays in the human genome.

Because Latimeria chalumnae and its relatives are so rare, scientists may never be able track down the evolutionary origins of the species 62 transposon-derived genes, but the latest discovery has already offered scientists insights into the ways transposons can move from species to species.

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