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Genome of ancient-looking fish gives clues to first limbed landlubbers

Aquamarine Fukushima

An African coelacanth, photographed using a Remotely Operated Vehicle off the coast of Tanga, Tanzania.

The genome of the coelacanth, an ancient-looking lobed-finned fish, has been sequenced and is already providing insight to the evolutionary changes that allowed the first four-limbed animals, called tetrapods, to crawl out of the water and on to land.

The sequence and preliminary analysis, reported Thursday in the journal Nature by a team spanning 40 research institutions and 12 countries, is a "massive piece of work," Xiaobo Xu, a paleontologist at Kean University who was not involved in the effort, told NBC News in an email.

"The paper really provides rare and valuable genomic data for offering heavy-weight opinions on issues bearing on the fish (to) tetrapod transition," he said.

It also settles a debate that has long raged amongst evolutionary biologists: what fish is the closest relative of tetrapods: the coelacanth or the equally odd-looking lobed-finned lungfish. The winner, according to analysis of the newly-published genome, is the lungfish.

"We think we have definitively shown it now," Jessica Alföldi, a research scientist at the Broad Institute of MIT and Harvard and co-first author of the paper, told NBC News. "They are very close, which is why it took so much data to figure it out."

Slow evolving genes
Scientists thought coelacanths went extinct about 70 million years ago, during the Late Cretaceous period. That changed when a fish trawler off the South African coast delivered a fresh-caught coelacanth to a local natural history museum in 1938, proving that the fish are alive and well.

The coelacanths' odd, ancient-looking looks raised eyebrows and earned it the nickname "living fossil" — much to the chagrin of evolutionary biologists, noted Alföldi. ("It makes people think there was no evolution," she explained.)

Analysis of the coelacanth genome reveals that the ancient fish is indeed evolving just about as quickly as all vertebrates in every aspect except one: its genes, the stretches of protein that code for specific functions.

Other aspects, such as the amount of transposable elements — so-called "junk DNA" — that jump around the genome, is about the same as other species, a sign of evolution. In addition, big chunks of DNA are constantly being rearranged. 

"But if we look at the proteins and say how much have these proteins changed in the last 400 million years, they have changed more in us than in the coelacanths, and they have changed a lot more in pretty much every other vertebrate species that we looked at," Alföldi said.

Why? 

One speculation is that coelacanths haven't needed to evolve, Alföldi said. They live in deep sea caves and appear to have few predators or competitors for food.

Fin to limb
Comparisons of the coelacanth genome with other vertebrates allows researchers to see what genes were lost and regulatory elements gained as lobed-finned fish crawled out of the sea and on to land. 

Some of the preliminary findings are expected, such as a suite of changes to regions of the genome that control limb development, for example. 

"This is consistent with the hypothesis that the autopod (the hand and digits) of land-living vertebrates is a modification of features already present in lobe-finned fishes, rather than something that arose entirely de novo," Matt Friedman, a paleobiologist at Oxford University, said in an email to NBC News.

Others, however, were unexpected, though "end up making total sense once you think about it," Alföldi said.

For example, genes related to smell exhibit a wide range of changes as vertebrates came on to land, which make sense given that smelling underwater is different than on land, she noted. Other changes are seen in sections of the genome that regulate immunity and the way fish and land animals poop.

For Friedman, who was not involved with the team, the findings are in line with decades of paleontological and anatomical studies of the coelacanths and other lobe-finned fish.

"Apart from specific genetic details — which are of course new — most of what is here seems to corroborate our current ideas about evolutionary changes associated with the origin of terrestriality," he said.

The specific genetic details will allow members of the research team and the broader scientific community to better understand what Yu called "the unique genomic features that shed light on the shared evolutionary past of lobe-finned fish and tetrapods."

John Roach is a contributing writer to NBC News. To learn more about him, visit his website