Coelacanth genome answers evolutionary questions

The coelacanth is one of the strangest Lazarus stories in modern science. This lobe-finned fish was thought to have been extinct for 65 million years until it was discovered amongst a fisherman’s catch by museum curator Marjorie Courtenay-Latimer in 1938. The fish, caught off the eastern coast of South Africa, had only ever been seen by scientists in the fossil record. A second species was found in a market in Indonesia in 1997. The coelacanth is a five-foot-long, blue or brown cave-dwelling fish and may hold the key to terrestrial tetrapod evolution.

This week, an international team of scientists announced that they had sequenced the DNA of the African coelacanth (Latimeria chalumnae). The genome of this ‘living fossil’ reinforced what scientists had long suspected: the genome of the coelacanth was evolving at a slower rate than that of other species. However, ‘living fossil’ is a misnomer. Species don’t live in a vacuum; the coelacanth has been living and evolving just as long as any other species on Earth. The only difference is the rate at which changes occur. According to Dr. Jessica Alföldi, co-lead author of the paper published in Nature this week, the genes of the coelacanth appear to change at a significantly slower rate than other vertebrates. One possible reason for this slow rate of change could be because coelacanths don’t need to change. These fish live in the deep waters off the eastern coast of Africa. Their habitat has not changed much over the past few million years and neither has the coelacanth.

Coelacanth at the Muséum d’Histoire Naturelle de Nantes (by sybarite48)

Sequencing the coelacanth genome has also allowed scientists to answer other nagging questions. For decades scientists have debated whether the coelacanth or the lungfish–another lobe-finned fish with ancient roots–is the basal tetrapodal ancestor. By comparing the DNA and RNA from coelacanth and lungfish to modern tetrapods, scientists concluded that the lungfish is more closely to related to terrestrial tetrapods than the coelacanth. That by no means lessens the coelacanth’s contributions to science. The unwieldy size of the lungfish genome (approximately 100 billion base pairs) makes it too long for scientists to effectively analyze. On the other hand, the genome of the coelacanth is a much more manageable length (similar to our own). That’s not to say that sequencing the coelacanth genome was easy. The African coelacanth is critically endangered, which means there were limited opportunities to do research. Any sample was a precious commodity that could not be wasted; there may not be another chance to sequence the genetic material.

Differences between the genome of the coelacanth and terrestrial tetrapods help to illuminate the changes that occurred with the transition to life on the land. Scientists made four key discoveries. First, they found differences in the regulatory genes involved with the sense of smell. Detecting odors in the air differs from detecting odors underwater and these changes reflect these differences. Secondly, there are key differences in regulatory genes involved with immunity. The transition to land exposed organisms to new pathogens and the genome had to adapt. Thirdly, scientists found regions of the genome had been ‘evolutionarily recruited’ to form the limbs of tetrapods, including arms, legs, fingers and toes. Specifically, ‘HoxD’ genes were likely used by tetrapods to makes those fleshy fins into limbs. Finally, scientists found that an essential gene in waste excretion differed between the coelacanth and tetrapods. This could be a clue to the genetics of the differences in methods of homeostasis: fish release ammonia directly into the water, while tetrapods convert ammonia into urea using the urea cycle. These insights are just the tip of the iceberg: the coelacanth genome likely still holds more keys to terrestrial evolution.

To learn more about the coelacanth genome, check out the link below.

Coelacanth genome surfaces

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