/ 9 May 2013

Coelacanth research gets a leg up

Rhodes University ichthyologist Professor JLB Smith with a coelacanth in 1953.
Rhodes University ichthyologist Professor JLB Smith with a coelacanth in 1953.

Until 1938, the ­coelacanth could be found only in textbooks or imprinted on rocks. But the rediscovery 75 years ago near East London of what has become known as the "fossil fish" has breathed life into the study of this fleshy-finned fish, which was thought to have died out 70-million years ago. Now, researchers have sequenced the genome of this "living fossil" – a project started in South Africa – to track the evolutionary chain from fish to human, as certain gene codes were lost and fins became feet.

About 400-million years ago animals shuffled out of oceans and onto land, marking one of the most important steps in our evolutionary history. But there is a gap in our understanding between animals on land and the first fish that crawled out of the sea.

African Coelacanth Ecosystem Programme (Acep) director Angus Paterson compared the creature's discovery to finding a living ­tyrannosaurus rex.

"Here is a creature we thought was extinct for 70-million years and then we catch one," he said.

Acep is a joint programme of the departments of science and technology and environmental affairs, the South African Institute for Aquatic Biodiversity, the South African Environmental Observation Network and the National Research Foundation.

Last month, 91 researchers published a paper in the journal Nature, detailing the sequencing of the African coelacanth genome.

Million-year-old ancestor
They concluded that the coelacanth – blue, prehistoric-looking and about 2m long – was not the "last fish", deciding that this title was better suited to the lungfish, but its genome was a "blueprint for tetrapod [four-limbed animals with a backbone] evolution", as it was so similar to its million-year-old ancestor.

Rosemary Dorrington, a professor in Rhodes University's department of biochemistry, microbiology and biotechnology, and visiting professor Gregory Blatch, began the genome project and were responsible for collecting the samples for testing.

Speaking from Marion Island, Dorrington told the Mail & Guardian that collecting samples was a challenge, because they couldn't catch any – coelacanths are protected. "Where it lives, we can't get to," she said. "And the regions in which it is found are among the poorest in the world, with no infrastructure".

Since 1938, African coelacanths,  known as Latimeria chalumnae, after Marjorie Courtney-Latimer who found the first coelacanth near Chalumna River in the Eastern Cape,  have been found in South Africa and the Comoros and sighted on the East African coast. In 1997, an Asian species, L. menadoenis, was discovered in Indonesia.

It was from the Comoros that a sample eventually came in 2003 – 10ml of blood taken from a coelacanth that had recently died.

Coelacanth genes
Dorrington said that when she and Blatch first embarked on the genome project they did not understand the scope of it. The genome is the same size as a human's. In 2003  the technology did not yet exist for rapid genome sequencing. So the project had to wait until "the technology could handle it", said Alan Christoffels, research chair in bioinformatics and health genomics at the University of the Western Cape, who was also involved in the project.

 As Dorrington put it, "The human genome project took 10 years and this project took six months."

The sequencing was done in the US, with American funding.

Christoffels's group looked at the collection of coelacanth genes that discriminate between taste and odour: "The coelacanth has genes that allow them to discriminate sweet tastes. It is the first fish [we've found] that can discriminate between these tastes," he said, noting that this trait made the fish similar to humans, but that researchers do not know why it has this ability.

Said Dorrington: "[The coelacanth] is the closest relative of dinosaurs and its genes have moved slower than ours, without evolutionary pressure pushing it one way or another. It is a snapshot of what we looked like [genetically] 400-million years ago. If we know how we got here, we know where we're going."