African Coelacanth Genome Sequenced: Evolutionary Clues from a Living Fossil

The African coelacanth is a living fossil, a fish from the past with limb-like fins. Once thought to have gone extinct, the fish was re-discovered in 1938. Since then, scientists have researched the ancient-looking creature. Now, they've sequenced the fish's genome and found some surprising insights about evolution.

The coelacanth is a rare order of fish that includes only two extant species, the West Indian Ocean coelacanth and the Indonesian coelacanth. One of the oldest known living lineage of lobe-finned fish, they're actually more closely related to lungfish, reptiles and mammals than to ray-finned fish. It's possible that a similar-looking creature eventually emerged from the water and walked early Earth, setting the stage for land species to evolve.

In order to learn more about this species, scientists sequenced nearly three billion "letters" of DNA from the coelacanth. The researchers also looked at RNA content from the coelacanth and from the lungfish. This allowed them to compare genes in use in the brain, kidneys, liver, spleen and gut of lungfish with the gene sets from coelacanth and 20 other vertebrate species.

What did they find? The researchers discovered that the genes in the coelacanth are evolving significantly more slowly than in every other fish and land vertebrate that they looked at.

"We often talk about how species changed over time," said Kerstin Lindblad-Tho, scientific director of the Broad Institute's vertebrate genome biology group and senior author, in a press release. "But there are still a few places on Earth where organisms don't have to change, and this is one of them. Coelacanths are likely very specialized to such a specific, non-changing extreme environment--it is ideally suited to the deep sea just the way it is."

In addition to learning that the coelacanth has evolved more slowly, the researchers also found valuable clues about the genetic changes that may have allowed tetrapods to flourish on land. More specifically, they discovered many regulatory changes influenced genes involved in smell perception. It's possible that as creatures moved from sea to land, they needed new means of detecting chemicals in the environment around them. In addition, the scientists noted that there were a significant number of immune-related regulatory changes when they compared the coelacanth genome to genomes of land animals. It's possible that these changes could be part of a response to new pathogens encountered on land.

Most likely, scientists will unearth further clues in the coelacanth genome as they examine it further, and the analysis could allow them to better understand the evolutionary transition from water to land.

"This is just the beginning of many analyses on what the coelacanth can teach us about the emergence of land vertebrates, including humans, and, combined with modern empirical approaches, can lend insights into the mechanisms that have contributed to major evolutionary innovations," said Chris Amemiya, co-author of the paper, in a press release.

The details of this study are published in the journal Nature.